{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Characterizing the general methylation landscape"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"In this notebook, I will characterize the general methylation landscape for each sex separately. To characterize CpG methylation, I will use individual samples, as well as a union BEDgraph that concatenates all sample information.\n",
"\n",
"1. Concatenate coverage information\n",
"2. Characterize methylation for each CpG dinucleotide in individual samples and union BEDgraph\n",
"2. Determine genomic location of highly methylated, moderately methylated, and lowly CpGs"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 0. Set working directory"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/Users/yaaminivenkataraman/Documents/ceabigr/code\r\n"
]
}
],
"source": [
"!pwd"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/Users/yaaminivenkataraman/Documents/ceabigr/output\n"
]
}
],
"source": [
"cd ../output/"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"mkdir: methylation-landscape: File exists\r\n"
]
}
],
"source": [
"!mkdir methylation-landscape"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/Users/yaaminivenkataraman/Documents/ceabigr/output/methylation-landscape\n"
]
}
],
"source": [
"cd methylation-landscape/"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"bedtoolsDirectory = \"/opt/homebrew/bin/\""
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0.25.1\n"
]
}
],
"source": [
"#Install pandas for this notebook\n",
"import pandas as pd\n",
"print(pd.__version__)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 1. Set up analysis"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 1a. Obtain sample bedGraphs"
]
},
{
"cell_type": "code",
"execution_count": 41,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"--2022-02-21 14:45:35-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/\n",
"Resolving gannet.fish.washington.edu (gannet.fish.washington.edu)... 128.95.149.52\n",
"Connecting to gannet.fish.washington.edu (gannet.fish.washington.edu)|128.95.149.52|:443... connected.\n",
"WARNING: cannot verify gannet.fish.washington.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:\n",
" Unable to locally verify the issuer's authority.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html.tmp’\n",
"\n",
"index.html.tmp [ <=> ] 62.99K --.-KB/s in 0.03s \n",
"\n",
"2022-02-21 14:45:41 (2.27 MB/s) - ‘./index.html.tmp’ saved [64500]\n",
"\n",
"Loading robots.txt; please ignore errors.\n",
"--2022-02-21 14:45:41-- https://gannet.fish.washington.edu/robots.txt\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 404 Not Found\n",
"2022-02-21 14:45:41 ERROR 404: Not Found.\n",
"\n",
"Removing ./index.html.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 14:45:41-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/?C=N;O=D\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=N;O=D.tmp’\n",
"\n",
"index.html?C=N;O=D. [ <=> ] 62.99K --.-KB/s in 0.03s \n",
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"2022-02-21 14:45:44 (2.39 MB/s) - ‘./index.html?C=N;O=D.tmp’ saved [64500]\n",
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"\n",
"--2022-02-21 14:45:44-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/?C=M;O=A\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
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"Saving to: ‘./index.html?C=M;O=A.tmp’\n",
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"2022-02-21 14:45:47 (1.98 MB/s) - ‘./index.html?C=M;O=A.tmp’ saved [64500]\n",
"\n",
"Removing ./index.html?C=M;O=A.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 14:45:47-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/?C=S;O=A\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=S;O=A.tmp’\n",
"\n",
"index.html?C=S;O=A. [ <=> ] 62.99K --.-KB/s in 0.02s \n",
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"2022-02-21 14:45:49 (2.53 MB/s) - ‘./index.html?C=S;O=A.tmp’ saved [64500]\n",
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"Removing ./index.html?C=S;O=A.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 14:45:49-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/?C=D;O=A\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=D;O=A.tmp’\n",
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"index.html?C=D;O=A. [ <=> ] 62.99K --.-KB/s in 0.03s \n",
"\n",
"2022-02-21 14:45:52 (2.44 MB/s) - ‘./index.html?C=D;O=A.tmp’ saved [64500]\n",
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"Removing ./index.html?C=D;O=A.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 14:45:52-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/3F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 324156781 (309M)\n",
"Saving to: ‘./3F_R1_val_1_10x.bedgraph’\n",
"\n",
"3F_R1_val_1_10x.bed 100%[===================>] 309.14M 7.19MB/s in 35s \n",
"\n",
"2022-02-21 14:46:27 (8.88 MB/s) - ‘./3F_R1_val_1_10x.bedgraph’ saved [324156781/324156781]\n",
"\n",
"--2022-02-21 14:46:28-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/6M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 288517292 (275M)\n",
"Saving to: ‘./6M_R1_val_1_10x.bedgraph’\n",
"\n",
"6M_R1_val_1_10x.bed 100%[===================>] 275.15M 7.32MB/s in 36s \n",
"\n",
"2022-02-21 14:47:04 (7.65 MB/s) - ‘./6M_R1_val_1_10x.bedgraph’ saved [288517292/288517292]\n",
"\n",
"--2022-02-21 14:47:05-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/7M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 306609326 (292M)\n",
"Saving to: ‘./7M_R1_val_1_10x.bedgraph’\n",
"\n",
"7M_R1_val_1_10x.bed 100%[===================>] 292.41M 6.82MB/s in 41s \n",
"\n",
"2022-02-21 14:47:46 (7.05 MB/s) - ‘./7M_R1_val_1_10x.bedgraph’ saved [306609326/306609326]\n",
"\n",
"--2022-02-21 14:47:47-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/9M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 298574740 (285M)\n",
"Saving to: ‘./9M_R1_val_1_10x.bedgraph’\n",
"\n",
"9M_R1_val_1_10x.bed 100%[===================>] 284.74M 7.62MB/s in 39s \n",
"\n",
"2022-02-21 14:48:26 (7.30 MB/s) - ‘./9M_R1_val_1_10x.bedgraph’ saved [298574740/298574740]\n",
"\n",
"--2022-02-21 14:48:27-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/12M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 327541717 (312M)\n",
"Saving to: ‘./12M_R1_val_1_10x.bedgraph’\n",
"\n",
"12M_R1_val_1_10x.be 100%[===================>] 312.37M 7.84MB/s in 41s \n",
"\n",
"2022-02-21 14:49:08 (7.70 MB/s) - ‘./12M_R1_val_1_10x.bedgraph’ saved [327541717/327541717]\n",
"\n",
"--2022-02-21 14:49:09-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/13M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 328207462 (313M)\n",
"Saving to: ‘./13M_R1_val_1_10x.bedgraph’\n",
"\n",
"13M_R1_val_1_10x.be 100%[===================>] 313.00M 8.19MB/s in 40s \n",
"\n",
"2022-02-21 14:49:49 (7.77 MB/s) - ‘./13M_R1_val_1_10x.bedgraph’ saved [328207462/328207462]\n",
"\n",
"--2022-02-21 14:49:50-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/16F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 321967648 (307M)\n",
"Saving to: ‘./16F_R1_val_1_10x.bedgraph’\n",
"\n",
"16F_R1_val_1_10x.be 100%[===================>] 307.05M 7.52MB/s in 39s \n",
"\n",
"2022-02-21 14:50:29 (7.95 MB/s) - ‘./16F_R1_val_1_10x.bedgraph’ saved [321967648/321967648]\n",
"\n",
"--2022-02-21 14:50:29-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/19F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 323592506 (309M)\n",
"Saving to: ‘./19F_R1_val_1_10x.bedgraph’\n",
"\n",
"19F_R1_val_1_10x.be 100%[===================>] 308.60M 8.40MB/s in 40s \n",
"\n",
"2022-02-21 14:51:10 (7.66 MB/s) - ‘./19F_R1_val_1_10x.bedgraph’ saved [323592506/323592506]\n",
"\n",
"--2022-02-21 14:51:11-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/22F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 296522791 (283M)\n",
"Saving to: ‘./22F_R1_val_1_10x.bedgraph’\n",
"\n",
"22F_R1_val_1_10x.be 100%[===================>] 282.79M 8.75MB/s in 34s \n",
"\n",
"2022-02-21 14:51:45 (8.22 MB/s) - ‘./22F_R1_val_1_10x.bedgraph’ saved [296522791/296522791]\n",
"\n",
"--2022-02-21 14:51:46-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/23M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 333001123 (318M)\n",
"Saving to: ‘./23M_R1_val_1_10x.bedgraph’\n",
"\n",
"23M_R1_val_1_10x.be 100%[===================>] 317.57M 8.21MB/s in 40s \n",
"\n",
"2022-02-21 14:52:26 (7.89 MB/s) - ‘./23M_R1_val_1_10x.bedgraph’ saved [333001123/333001123]\n",
"\n",
"--2022-02-21 14:52:27-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/29F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 309248216 (295M)\n",
"Saving to: ‘./29F_R1_val_1_10x.bedgraph’\n",
"\n",
"29F_R1_val_1_10x.be 100%[===================>] 294.92M 8.77MB/s in 37s \n",
"\n",
"2022-02-21 14:53:04 (7.98 MB/s) - ‘./29F_R1_val_1_10x.bedgraph’ saved [309248216/309248216]\n",
"\n",
"--2022-02-21 14:53:05-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/31M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 302169302 (288M)\n",
"Saving to: ‘./31M_R1_val_1_10x.bedgraph’\n",
"\n",
"31M_R1_val_1_10x.be 100%[===================>] 288.17M 7.97MB/s in 35s \n",
"\n",
"2022-02-21 14:53:40 (8.30 MB/s) - ‘./31M_R1_val_1_10x.bedgraph’ saved [302169302/302169302]\n",
"\n",
"--2022-02-21 14:53:40-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/35F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 315211011 (301M)\n",
"Saving to: ‘./35F_R1_val_1_10x.bedgraph’\n",
"\n",
"35F_R1_val_1_10x.be 100%[===================>] 300.61M 2.39MB/s in 91s \n",
"\n",
"2022-02-21 14:55:11 (3.32 MB/s) - ‘./35F_R1_val_1_10x.bedgraph’ saved [315211011/315211011]\n",
"\n",
"--2022-02-21 14:55:12-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/36F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 318668814 (304M)\n",
"Saving to: ‘./36F_R1_val_1_10x.bedgraph’\n",
"\n",
"36F_R1_val_1_10x.be 100%[===================>] 303.91M 9.29MB/s in 37s \n",
"\n",
"2022-02-21 14:55:49 (8.25 MB/s) - ‘./36F_R1_val_1_10x.bedgraph’ saved [318668814/318668814]\n",
"\n",
"--2022-02-21 14:55:49-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/39F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 308813092 (295M)\n",
"Saving to: ‘./39F_R1_val_1_10x.bedgraph’\n",
"\n",
"39F_R1_val_1_10x.be 100%[===================>] 294.51M 7.30MB/s in 41s \n",
"\n",
"2022-02-21 14:56:30 (7.24 MB/s) - ‘./39F_R1_val_1_10x.bedgraph’ saved [308813092/308813092]\n",
"\n",
"--2022-02-21 14:56:31-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/41F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 266487354 (254M)\n",
"Saving to: ‘./41F_R1_val_1_10x.bedgraph’\n",
"\n",
"41F_R1_val_1_10x.be 100%[===================>] 254.14M 7.52MB/s in 31s \n",
"\n",
"2022-02-21 14:57:02 (8.30 MB/s) - ‘./41F_R1_val_1_10x.bedgraph’ saved [266487354/266487354]\n",
"\n",
"--2022-02-21 14:57:02-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/44F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 365352164 (348M)\n",
"Saving to: ‘./44F_R1_val_1_10x.bedgraph’\n",
"\n",
"44F_R1_val_1_10x.be 100%[===================>] 348.43M 11.9MB/s in 41s \n",
"\n",
"2022-02-21 14:57:43 (8.57 MB/s) - ‘./44F_R1_val_1_10x.bedgraph’ saved [365352164/365352164]\n",
"\n",
"--2022-02-21 14:57:44-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/48M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 307861120 (294M)\n",
"Saving to: ‘./48M_R1_val_1_10x.bedgraph’\n",
"\n",
"48M_R1_val_1_10x.be 100%[===================>] 293.60M 6.97MB/s in 37s \n",
"\n",
"2022-02-21 14:58:21 (7.99 MB/s) - ‘./48M_R1_val_1_10x.bedgraph’ saved [307861120/307861120]\n",
"\n",
"--2022-02-21 14:58:22-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/50F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 315815151 (301M)\n",
"Saving to: ‘./50F_R1_val_1_10x.bedgraph’\n",
"\n",
"50F_R1_val_1_10x.be 100%[===================>] 301.18M 8.55MB/s in 45s \n",
"\n",
"2022-02-21 14:59:06 (6.73 MB/s) - ‘./50F_R1_val_1_10x.bedgraph’ saved [315815151/315815151]\n",
"\n",
"--2022-02-21 14:59:07-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/52F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 325800111 (311M)\n",
"Saving to: ‘./52F_R1_val_1_10x.bedgraph’\n",
"\n",
"52F_R1_val_1_10x.be 100%[===================>] 310.71M 5.12MB/s in 44s \n",
"\n",
"2022-02-21 14:59:52 (7.02 MB/s) - ‘./52F_R1_val_1_10x.bedgraph’ saved [325800111/325800111]\n",
"\n",
"--2022-02-21 14:59:52-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/53F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 323430938 (308M)\n",
"Saving to: ‘./53F_R1_val_1_10x.bedgraph’\n",
"\n",
"53F_R1_val_1_10x.be 100%[===================>] 308.45M 7.53MB/s in 39s \n",
"\n",
"2022-02-21 15:00:31 (8.00 MB/s) - ‘./53F_R1_val_1_10x.bedgraph’ saved [323430938/323430938]\n",
"\n",
"--2022-02-21 15:00:32-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/54F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 326698067 (312M)\n",
"Saving to: ‘./54F_R1_val_1_10x.bedgraph’\n",
"\n",
"54F_R1_val_1_10x.be 100%[===================>] 311.56M 7.55MB/s in 43s \n",
"\n",
"2022-02-21 15:01:14 (7.32 MB/s) - ‘./54F_R1_val_1_10x.bedgraph’ saved [326698067/326698067]\n",
"\n",
"--2022-02-21 15:01:15-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/59M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 275550232 (263M)\n",
"Saving to: ‘./59M_R1_val_1_10x.bedgraph’\n",
"\n",
"59M_R1_val_1_10x.be 100%[===================>] 262.79M 9.33MB/s in 33s \n",
"\n",
"2022-02-21 15:01:48 (7.96 MB/s) - ‘./59M_R1_val_1_10x.bedgraph’ saved [275550232/275550232]\n",
"\n",
"--2022-02-21 15:01:49-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/64M_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 315360784 (301M)\n",
"Saving to: ‘./64M_R1_val_1_10x.bedgraph’\n",
"\n",
"64M_R1_val_1_10x.be 100%[===================>] 300.75M 11.4MB/s in 32s \n",
"\n",
"2022-02-21 15:02:22 (9.26 MB/s) - ‘./64M_R1_val_1_10x.bedgraph’ saved [315360784/315360784]\n",
"\n",
"--2022-02-21 15:02:23-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/76F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 310467003 (296M)\n",
"Saving to: ‘./76F_R1_val_1_10x.bedgraph’\n",
"\n",
"76F_R1_val_1_10x.be 100%[===================>] 296.08M 6.58MB/s in 34s \n",
"\n",
"2022-02-21 15:02:56 (8.82 MB/s) - ‘./76F_R1_val_1_10x.bedgraph’ saved [310467003/310467003]\n",
"\n",
"--2022-02-21 15:02:57-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/77F_R1_val_1_10x.bedgraph\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 319604216 (305M)\n",
"Saving to: ‘./77F_R1_val_1_10x.bedgraph’\n",
"\n",
"77F_R1_val_1_10x.be 100%[===================>] 304.80M 6.50MB/s in 43s \n",
"\n",
"2022-02-21 15:03:40 (7.13 MB/s) - ‘./77F_R1_val_1_10x.bedgraph’ saved [319604216/319604216]\n",
"\n",
"--2022-02-21 15:03:41-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/?C=N;O=A\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=N;O=A.tmp’\n",
"\n",
"index.html?C=N;O=A. [ <=> ] 62.99K --.-KB/s in 0.02s \n",
"\n",
"2022-02-21 15:03:44 (2.62 MB/s) - ‘./index.html?C=N;O=A.tmp’ saved [64500]\n",
"\n",
"Removing ./index.html?C=N;O=A.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:03:44-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/?C=M;O=D\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=M;O=D.tmp’\n",
"\n",
"index.html?C=M;O=D. [ <=> ] 62.99K --.-KB/s in 0.03s \n",
"\n",
"2022-02-21 15:03:46 (1.84 MB/s) - ‘./index.html?C=M;O=D.tmp’ saved [64500]\n",
"\n",
"Removing ./index.html?C=M;O=D.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:03:46-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/?C=S;O=D\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=S;O=D.tmp’\n",
"\n",
"index.html?C=S;O=D. [ <=> ] 62.99K --.-KB/s in 0.03s \n",
"\n",
"2022-02-21 15:03:49 (2.12 MB/s) - ‘./index.html?C=S;O=D.tmp’ saved [64500]\n",
"\n",
"Removing ./index.html?C=S;O=D.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:03:49-- https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/?C=D;O=D\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=D;O=D.tmp’\n",
"\n",
"index.html?C=D;O=D. [ <=> ] 62.99K --.-KB/s in 0.03s \n",
"\n",
"2022-02-21 15:03:52 (2.11 MB/s) - ‘./index.html?C=D;O=D.tmp’ saved [64500]\n",
"\n",
"Removing ./index.html?C=D;O=D.tmp since it should be rejected.\n",
"\n",
"FINISHED --2022-02-21 15:03:52--\n",
"Total wall clock time: 18m 17s\n",
"Downloaded: 35 files, 7.6G in 17m 26s (7.44 MB/s)\n"
]
}
],
"source": [
"#Download 10x bedgraphs\n",
"!wget -r \\\n",
"--no-check-certificate --no-directories --no-parent --reject \"index.html*\" \\\n",
"-P . \\\n",
"-A \"*10x.bedgraph\" https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/"
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"12M_R1_val_1_10x.bedgraph 36F_R1_val_1_10x.bedgraph 54F_R1_val_1_10x.bedgraph\r\n",
"13M_R1_val_1_10x.bedgraph 39F_R1_val_1_10x.bedgraph 59M_R1_val_1_10x.bedgraph\r\n",
"16F_R1_val_1_10x.bedgraph 3F_R1_val_1_10x.bedgraph 64M_R1_val_1_10x.bedgraph\r\n",
"19F_R1_val_1_10x.bedgraph 41F_R1_val_1_10x.bedgraph 6M_R1_val_1_10x.bedgraph\r\n",
"22F_R1_val_1_10x.bedgraph 44F_R1_val_1_10x.bedgraph 76F_R1_val_1_10x.bedgraph\r\n",
"23M_R1_val_1_10x.bedgraph 48M_R1_val_1_10x.bedgraph 77F_R1_val_1_10x.bedgraph\r\n",
"29F_R1_val_1_10x.bedgraph 50F_R1_val_1_10x.bedgraph 7M_R1_val_1_10x.bedgraph\r\n",
"31M_R1_val_1_10x.bedgraph 52F_R1_val_1_10x.bedgraph 9M_R1_val_1_10x.bedgraph\r\n",
"35F_R1_val_1_10x.bedgraph 53F_R1_val_1_10x.bedgraph\r\n"
]
}
],
"source": [
"#Check directory for all files\n",
"!ls"
]
},
{
"cell_type": "code",
"execution_count": 43,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"MD5 (12M_R1_val_1_10x.bedgraph) = 23710e666ba1d8d0aff05465a7ec143d\n",
"MD5 (13M_R1_val_1_10x.bedgraph) = 895d0b04d434e9567e648689e734308e\n",
"MD5 (16F_R1_val_1_10x.bedgraph) = 5e031b5c1aac89336d1a1a32c84383ff\n",
"MD5 (19F_R1_val_1_10x.bedgraph) = ad8e874af92071a08a9fc0e5cd31c959\n",
"MD5 (22F_R1_val_1_10x.bedgraph) = a34054b0cedf5b219e1a7f236571f882\n",
"MD5 (23M_R1_val_1_10x.bedgraph) = 8b5aa08e26db26865b35090e69c27ce0\n",
"MD5 (29F_R1_val_1_10x.bedgraph) = cda12bdb3ac9a2a304005d496c8d641b\n",
"MD5 (31M_R1_val_1_10x.bedgraph) = 6ea9d16b7c88775863e5f890144d900b\n",
"MD5 (35F_R1_val_1_10x.bedgraph) = fc230a6475afe86a21a99f70ddd51012\n",
"MD5 (36F_R1_val_1_10x.bedgraph) = bb83960173d236e832183e7b7a641156\n",
"MD5 (39F_R1_val_1_10x.bedgraph) = de0e77ea6da72f370dca9d5b09d7b1f3\n",
"MD5 (3F_R1_val_1_10x.bedgraph) = 7be44c21611319f59cfa94eec5a84851\n",
"MD5 (41F_R1_val_1_10x.bedgraph) = c3e39faa21463fdecafd78eb6f17b51a\n",
"MD5 (44F_R1_val_1_10x.bedgraph) = cd82809a568298c8cc84f7c8ab0a1fa7\n",
"MD5 (48M_R1_val_1_10x.bedgraph) = beeb7af3ab210324b787e6b50eed5f75\n",
"MD5 (50F_R1_val_1_10x.bedgraph) = 5601e78a8e8dffb3ccdb7f111e27bc16\n",
"MD5 (52F_R1_val_1_10x.bedgraph) = 7aa285958a26357e4a77154abb91fcc5\n",
"MD5 (53F_R1_val_1_10x.bedgraph) = ff306becacc03ed74976131671c9d05a\n",
"MD5 (54F_R1_val_1_10x.bedgraph) = 0ffe4633751e283b6d353751da22e920\n",
"MD5 (59M_R1_val_1_10x.bedgraph) = 67a745cd172d090eae8a305c236d15c2\n",
"MD5 (64M_R1_val_1_10x.bedgraph) = c5ed737cd2bf792e5621a2518054edf0\n",
"MD5 (6M_R1_val_1_10x.bedgraph) = 394d556f9d8dfc003e1c2746e7bf186c\n",
"MD5 (76F_R1_val_1_10x.bedgraph) = 51913b4116a0e787cdd4a25d12050dd3\n",
"MD5 (77F_R1_val_1_10x.bedgraph) = 01faf676ba5b30141a82c72acfb85e66\n",
"MD5 (7M_R1_val_1_10x.bedgraph) = e60f1eeac4818b96ee22785e1feb7a8e\n",
"MD5 (9M_R1_val_1_10x.bedgraph) = c5f60340edb87bb4135d668d39785f75\n"
]
}
],
"source": [
"#Obtain md5\n",
"!md5 *"
]
},
{
"cell_type": "code",
"execution_count": 44,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"\n",
"for f in *10x.bedgraph\n",
"do\n",
"/opt/homebrew/bin/sortBed \\\n",
"-i ${f} \\\n",
"> $(basename ${f%_10x.bedgraph})_10x.sort.bedgraph\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"scrolled": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"12M_R1_val_1_10x.sort.bedgraph 44F_R1_val_1_10x.sort.bedgraph\r\n",
"13M_R1_val_1_10x.sort.bedgraph 48M_R1_val_1_10x.sort.bedgraph\r\n",
"16F_R1_val_1_10x.sort.bedgraph 50F_R1_val_1_10x.sort.bedgraph\r\n",
"19F_R1_val_1_10x.sort.bedgraph 52F_R1_val_1_10x.sort.bedgraph\r\n",
"22F_R1_val_1_10x.sort.bedgraph 53F_R1_val_1_10x.sort.bedgraph\r\n",
"23M_R1_val_1_10x.sort.bedgraph 54F_R1_val_1_10x.sort.bedgraph\r\n",
"29F_R1_val_1_10x.sort.bedgraph 59M_R1_val_1_10x.sort.bedgraph\r\n",
"31M_R1_val_1_10x.sort.bedgraph 64M_R1_val_1_10x.sort.bedgraph\r\n",
"35F_R1_val_1_10x.sort.bedgraph 6M_R1_val_1_10x.sort.bedgraph\r\n",
"36F_R1_val_1_10x.sort.bedgraph 76F_R1_val_1_10x.sort.bedgraph\r\n",
"39F_R1_val_1_10x.sort.bedgraph 77F_R1_val_1_10x.sort.bedgraph\r\n",
"3F_R1_val_1_10x.sort.bedgraph 7M_R1_val_1_10x.sort.bedgraph\r\n",
"41F_R1_val_1_10x.sort.bedgraph 9M_R1_val_1_10x.sort.bedgraph\r\n"
]
}
],
"source": [
"!ls *sort*"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 1b. Remove C->T SNPs"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"For each sample, I will use BS-Snper output to change the percent methylation for a C->T SNP to 0."
]
},
{
"cell_type": "code",
"execution_count": 46,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"--2022-02-21 15:07:09-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/\n",
"Resolving gannet.fish.washington.edu (gannet.fish.washington.edu)... 128.95.149.52\n",
"Connecting to gannet.fish.washington.edu (gannet.fish.washington.edu)|128.95.149.52|:443... connected.\n",
"WARNING: cannot verify gannet.fish.washington.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:\n",
" Unable to locally verify the issuer's authority.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html.tmp’\n",
"\n",
"index.html.tmp [ <=> ] 32.59K --.-KB/s in 0.02s \n",
"\n",
"2022-02-21 15:07:11 (1.89 MB/s) - ‘./index.html.tmp’ saved [33377]\n",
"\n",
"Loading robots.txt; please ignore errors.\n",
"--2022-02-21 15:07:11-- https://gannet.fish.washington.edu/robots.txt\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 404 Not Found\n",
"2022-02-21 15:07:11 ERROR 404: Not Found.\n",
"\n",
"Removing ./index.html.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:07:11-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/?C=N;O=D\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=N;O=D.tmp’\n",
"\n",
"index.html?C=N;O=D. [ <=> ] 32.59K --.-KB/s in 0.01s \n",
"\n",
"2022-02-21 15:07:11 (2.52 MB/s) - ‘./index.html?C=N;O=D.tmp’ saved [33377]\n",
"\n",
"Removing ./index.html?C=N;O=D.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:07:11-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/?C=M;O=A\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=M;O=A.tmp’\n",
"\n",
"index.html?C=M;O=A. [ <=> ] 32.59K --.-KB/s in 0.01s \n",
"\n",
"2022-02-21 15:07:11 (2.96 MB/s) - ‘./index.html?C=M;O=A.tmp’ saved [33377]\n",
"\n",
"Removing ./index.html?C=M;O=A.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:07:11-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/?C=S;O=A\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=S;O=A.tmp’\n",
"\n",
"index.html?C=S;O=A. [ <=> ] 32.59K --.-KB/s in 0.02s \n",
"\n",
"2022-02-21 15:07:11 (2.02 MB/s) - ‘./index.html?C=S;O=A.tmp’ saved [33377]\n",
"\n",
"Removing ./index.html?C=S;O=A.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:07:11-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/?C=D;O=A\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=D;O=A.tmp’\n",
"\n",
"index.html?C=D;O=A. [ <=> ] 32.59K --.-KB/s in 0.01s \n",
"\n",
"2022-02-21 15:07:11 (2.98 MB/s) - ‘./index.html?C=D;O=A.tmp’ saved [33377]\n",
"\n",
"Removing ./index.html?C=D;O=A.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:07:11-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/3F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 465312493 (444M) [text/x-vcard]\n",
"Saving to: ‘./3F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"3F_R1_val_1_bismark 100%[===================>] 443.76M 8.71MB/s in 48s \n",
"\n",
"2022-02-21 15:08:00 (9.15 MB/s) - ‘./3F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [465312493/465312493]\n",
"\n",
"--2022-02-21 15:08:00-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/6M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 467743103 (446M) [text/x-vcard]\n",
"Saving to: ‘./6M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"6M_R1_val_1_bismark 100%[===================>] 446.07M 7.72MB/s in 52s \n",
"\n",
"2022-02-21 15:08:51 (8.66 MB/s) - ‘./6M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [467743103/467743103]\n",
"\n",
"--2022-02-21 15:08:51-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/7M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 487616586 (465M) [text/x-vcard]\n",
"Saving to: ‘./7M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"7M_R1_val_1_bismark 100%[===================>] 465.03M 7.53MB/s in 55s \n",
"\n",
"2022-02-21 15:09:47 (8.39 MB/s) - ‘./7M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [487616586/487616586]\n",
"\n",
"--2022-02-21 15:09:47-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/9M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 466809631 (445M) [text/x-vcard]\n",
"Saving to: ‘./9M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"9M_R1_val_1_bismark 100%[===================>] 445.18M 7.44MB/s in 61s \n",
"\n",
"2022-02-21 15:10:48 (7.29 MB/s) - ‘./9M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [466809631/466809631]\n",
"\n",
"--2022-02-21 15:10:48-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/12M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 527167569 (503M) [text/x-vcard]\n",
"Saving to: ‘./12M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"12M_R1_val_1_bismar 100%[===================>] 502.75M 6.49MB/s in 71s \n",
"\n",
"2022-02-21 15:11:59 (7.05 MB/s) - ‘./12M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [527167569/527167569]\n",
"\n",
"--2022-02-21 15:11:59-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/13M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 525639529 (501M) [text/x-vcard]\n",
"Saving to: ‘./13M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"13M_R1_val_1_bismar 100%[===================>] 501.29M 8.24MB/s in 69s \n",
"\n",
"2022-02-21 15:13:08 (7.27 MB/s) - ‘./13M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [525639529/525639529]\n",
"\n",
"--2022-02-21 15:13:08-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/16F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 524786589 (500M) [text/x-vcard]\n",
"Saving to: ‘./16F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"16F_R1_val_1_bismar 100%[===================>] 500.47M 7.66MB/s in 69s \n",
"\n",
"2022-02-21 15:14:17 (7.26 MB/s) - ‘./16F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [524786589/524786589]\n",
"\n",
"--2022-02-21 15:14:17-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/19F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 528278513 (504M) [text/x-vcard]\n",
"Saving to: ‘./19F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"19F_R1_val_1_bismar 100%[===================>] 503.80M 6.36MB/s in 72s \n",
"\n",
"2022-02-21 15:15:29 (7.01 MB/s) - ‘./19F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [528278513/528278513]\n",
"\n",
"--2022-02-21 15:15:29-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/22F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 477683220 (456M) [text/x-vcard]\n",
"Saving to: ‘./22F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"22F_R1_val_1_bismar 100%[===================>] 455.55M 7.75MB/s in 64s \n",
"\n",
"2022-02-21 15:16:33 (7.10 MB/s) - ‘./22F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [477683220/477683220]\n",
"\n",
"--2022-02-21 15:16:33-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/23M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 537035183 (512M) [text/x-vcard]\n",
"Saving to: ‘./23M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"23M_R1_val_1_bismar 100%[===================>] 512.16M 7.35MB/s in 70s \n",
"\n",
"2022-02-21 15:17:44 (7.32 MB/s) - ‘./23M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [537035183/537035183]\n",
"\n",
"--2022-02-21 15:17:44-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/29F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 492776744 (470M) [text/x-vcard]\n",
"Saving to: ‘./29F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"29F_R1_val_1_bismar 100%[===================>] 469.95M 8.65MB/s in 55s \n",
"\n",
"2022-02-21 15:18:39 (8.49 MB/s) - ‘./29F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [492776744/492776744]\n",
"\n",
"--2022-02-21 15:18:39-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/31M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 444037747 (423M) [text/x-vcard]\n",
"Saving to: ‘./31M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"31M_R1_val_1_bismar 100%[===================>] 423.47M 8.57MB/s in 45s \n",
"\n",
"2022-02-21 15:19:25 (9.34 MB/s) - ‘./31M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [444037747/444037747]\n",
"\n",
"--2022-02-21 15:19:25-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/35F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 510177870 (487M) [text/x-vcard]\n",
"Saving to: ‘./35F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"35F_R1_val_1_bismar 100%[===================>] 486.54M 8.36MB/s in 56s \n",
"\n",
"2022-02-21 15:20:21 (8.71 MB/s) - ‘./35F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [510177870/510177870]\n",
"\n",
"--2022-02-21 15:20:21-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/36F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 512327646 (489M) [text/x-vcard]\n",
"Saving to: ‘./36F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"36F_R1_val_1_bismar 100%[===================>] 488.59M 8.48MB/s in 60s \n",
"\n",
"2022-02-21 15:21:21 (8.16 MB/s) - ‘./36F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [512327646/512327646]\n",
"\n",
"--2022-02-21 15:21:21-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/39F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 499746037 (477M) [text/x-vcard]\n",
"Saving to: ‘./39F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"39F_R1_val_1_bismar 100%[===================>] 476.59M 8.69MB/s in 57s \n",
"\n",
"2022-02-21 15:22:18 (8.34 MB/s) - ‘./39F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [499746037/499746037]\n",
"\n",
"--2022-02-21 15:22:18-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/41F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 443849745 (423M) [text/x-vcard]\n",
"Saving to: ‘./41F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"41F_R1_val_1_bismar 100%[===================>] 423.29M 8.96MB/s in 54s \n",
"\n",
"2022-02-21 15:23:12 (7.87 MB/s) - ‘./41F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [443849745/443849745]\n",
"\n",
"--2022-02-21 15:23:12-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/44F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 625518839 (597M) [text/x-vcard]\n",
"Saving to: ‘./44F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"44F_R1_val_1_bismar 100%[===================>] 596.54M 8.92MB/s in 68s \n",
"\n",
"2022-02-21 15:24:20 (8.80 MB/s) - ‘./44F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [625518839/625518839]\n",
"\n",
"--2022-02-21 15:24:20-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/48M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 504794537 (481M) [text/x-vcard]\n",
"Saving to: ‘./48M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"48M_R1_val_1_bismar 100%[===================>] 481.41M 8.49MB/s in 55s \n",
"\n",
"2022-02-21 15:25:14 (8.82 MB/s) - ‘./48M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [504794537/504794537]\n",
"\n",
"--2022-02-21 15:25:14-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/50F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 497505228 (474M) [text/x-vcard]\n",
"Saving to: ‘./50F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"50F_R1_val_1_bismar 100%[===================>] 474.46M 8.56MB/s in 55s \n",
"\n",
"2022-02-21 15:26:09 (8.63 MB/s) - ‘./50F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [497505228/497505228]\n",
"\n",
"--2022-02-21 15:26:09-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/52F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 523919766 (500M) [text/x-vcard]\n",
"Saving to: ‘./52F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"52F_R1_val_1_bismar 100%[===================>] 499.65M 8.88MB/s in 57s \n",
"\n",
"2022-02-21 15:27:06 (8.82 MB/s) - ‘./52F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [523919766/523919766]\n",
"\n",
"--2022-02-21 15:27:06-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/53F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 523892456 (500M) [text/x-vcard]\n",
"Saving to: ‘./53F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"53F_R1_val_1_bismar 100%[===================>] 499.62M 9.43MB/s in 57s \n",
"\n",
"2022-02-21 15:28:03 (8.81 MB/s) - ‘./53F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [523892456/523892456]\n",
"\n",
"--2022-02-21 15:28:03-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/54F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 528366556 (504M) [text/x-vcard]\n",
"Saving to: ‘./54F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"54F_R1_val_1_bismar 100%[===================>] 503.89M 9.05MB/s in 57s \n",
"\n",
"2022-02-21 15:29:00 (8.86 MB/s) - ‘./54F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [528366556/528366556]\n",
"\n",
"--2022-02-21 15:29:00-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/59M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 458293811 (437M) [text/x-vcard]\n",
"Saving to: ‘./59M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"59M_R1_val_1_bismar 100%[===================>] 437.06M 8.83MB/s in 50s \n",
"\n",
"2022-02-21 15:29:50 (8.73 MB/s) - ‘./59M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [458293811/458293811]\n",
"\n",
"--2022-02-21 15:29:50-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/64M_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 503318890 (480M) [text/x-vcard]\n",
"Saving to: ‘./64M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"64M_R1_val_1_bismar 100%[===================>] 480.00M 9.54MB/s in 52s \n",
"\n",
"2022-02-21 15:30:42 (9.15 MB/s) - ‘./64M_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [503318890/503318890]\n",
"\n",
"--2022-02-21 15:30:42-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/76F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 494986093 (472M) [text/x-vcard]\n",
"Saving to: ‘./76F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"76F_R1_val_1_bismar 100%[===================>] 472.05M 7.76MB/s in 53s \n",
"\n",
"2022-02-21 15:31:35 (8.92 MB/s) - ‘./76F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [494986093/494986093]\n",
"\n",
"--2022-02-21 15:31:35-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/77F_R1_val_1_bismark_bt2_pe.SNP-results.vcf\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 518123700 (494M) [text/x-vcard]\n",
"Saving to: ‘./77F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’\n",
"\n",
"77F_R1_val_1_bismar 100%[===================>] 494.12M 7.94MB/s in 57s \n",
"\n",
"2022-02-21 15:32:33 (8.60 MB/s) - ‘./77F_R1_val_1_bismark_bt2_pe.SNP-results.vcf’ saved [518123700/518123700]\n",
"\n",
"--2022-02-21 15:32:33-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/?C=N;O=A\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=N;O=A.tmp’\n",
"\n",
"index.html?C=N;O=A. [ <=> ] 32.59K --.-KB/s in 0.01s \n",
"\n",
"2022-02-21 15:32:34 (2.60 MB/s) - ‘./index.html?C=N;O=A.tmp’ saved [33377]\n",
"\n",
"Removing ./index.html?C=N;O=A.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:32:34-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/?C=M;O=D\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=M;O=D.tmp’\n",
"\n",
"index.html?C=M;O=D. [ <=> ] 32.59K --.-KB/s in 0.01s \n",
"\n",
"2022-02-21 15:32:34 (3.07 MB/s) - ‘./index.html?C=M;O=D.tmp’ saved [33377]\n",
"\n",
"Removing ./index.html?C=M;O=D.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:32:34-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/?C=S;O=D\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=S;O=D.tmp’\n",
"\n",
"index.html?C=S;O=D. [ <=> ] 32.59K --.-KB/s in 0.009s \n",
"\n",
"2022-02-21 15:32:34 (3.36 MB/s) - ‘./index.html?C=S;O=D.tmp’ saved [33377]\n",
"\n",
"Removing ./index.html?C=S;O=D.tmp since it should be rejected.\n",
"\n",
"--2022-02-21 15:32:34-- https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/?C=D;O=D\n",
"Reusing existing connection to gannet.fish.washington.edu:443.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [text/html]\n",
"Saving to: ‘./index.html?C=D;O=D.tmp’\n",
"\n",
"index.html?C=D;O=D. [ <=> ] 32.59K --.-KB/s in 0.008s \n",
"\n",
"2022-02-21 15:32:34 (3.88 MB/s) - ‘./index.html?C=D;O=D.tmp’ saved [33377]\n",
"\n",
"Removing ./index.html?C=D;O=D.tmp since it should be rejected.\n",
"\n",
"FINISHED --2022-02-21 15:32:34--\n",
"Total wall clock time: 25m 25s\n",
"Downloaded: 35 files, 12G in 25m 20s (8.21 MB/s)\n"
]
}
],
"source": [
"#Download 10x SNP\n",
"!wget -r \\\n",
"--no-check-certificate --no-directories --no-parent --reject \"index.html*\" \\\n",
"-P . \\\n",
"-A \"*vcf\" https://gannet.fish.washington.edu/seashell/bu-github/nb-2022/C_virginica/analyses/bsnp02/"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"\n",
"for f in *10x.sort.bedgraph\n",
"do\n",
"awk -F\"\\t\" 'NR==FNR{a[$1\"\\t\"$2]=$1\"\\t\"$2;next}{if(($1\"\\t\"$2) in a) print $1\"\\t\"$2\"\\t\"$3\"\\t\"0;else print $0}' \\\n",
"$(basename ${f%_10x.sort.bedgraph})_bismark_bt2_pe.SNP-results.vcf \\\n",
"${f} \\\n",
"> $(basename ${f%_10x.sort.bedgraph})_10x.SNPcorr.bedgraph\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"12M_R1_val_1_10x.SNPcorr.bedgraph 44F_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"13M_R1_val_1_10x.SNPcorr.bedgraph 48M_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"16F_R1_val_1_10x.SNPcorr.bedgraph 50F_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"19F_R1_val_1_10x.SNPcorr.bedgraph 52F_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"22F_R1_val_1_10x.SNPcorr.bedgraph 53F_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"23M_R1_val_1_10x.SNPcorr.bedgraph 54F_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"29F_R1_val_1_10x.SNPcorr.bedgraph 59M_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"31M_R1_val_1_10x.SNPcorr.bedgraph 64M_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"35F_R1_val_1_10x.SNPcorr.bedgraph 6M_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"36F_R1_val_1_10x.SNPcorr.bedgraph 76F_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"39F_R1_val_1_10x.SNPcorr.bedgraph 77F_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"3F_R1_val_1_10x.SNPcorr.bedgraph 7M_R1_val_1_10x.SNPcorr.bedgraph\r\n",
"41F_R1_val_1_10x.SNPcorr.bedgraph 9M_R1_val_1_10x.SNPcorr.bedgraph\r\n"
]
}
],
"source": [
"!ls *10x.SNPcorr.bedgraph"
]
},
{
"cell_type": "code",
"execution_count": 44,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"\n",
"for f in *10x.sort.bedgraph\n",
"do\n",
"/opt/homebrew/bin/intersectBed \\\n",
"-wa \\\n",
"-a ${f} \\\n",
"-b $(basename ${f%_10x.sort.bedgraph})_bismark_bt2_pe.SNP-results.vcf \\\n",
"> $(basename ${f%_10x.sort.bedgraph})_10x.SNPcorr.changedpos.bedgraph\n",
"done"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 2. General methylation landscape"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 2a. Create a union BEDgraph"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"I will use `unionBedGraphs` to concatenate information for all loci across samples. This will be use in separate analyses."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\r\n",
"Tool: bedtools unionbedg (aka unionBedGraphs)\r\n",
"Version: v2.30.0\r\n",
"Summary: Combines multiple BedGraph files into a single file,\r\n",
"\t allowing coverage comparisons between them.\r\n",
"\r\n",
"Usage: bedtools unionbedg [OPTIONS] -i FILE1 FILE2 .. FILEn\r\n",
"\t Assumes that each BedGraph file is sorted by chrom/start \r\n",
"\t and that the intervals in each are non-overlapping.\r\n",
"\r\n",
"Options: \r\n",
"\t-header\t\tPrint a header line.\r\n",
"\t\t\t(chrom/start/end + names of each file).\r\n",
"\r\n",
"\t-names\t\tA list of names (one/file) to describe each file in -i.\r\n",
"\t\t\tThese names will be printed in the header line.\r\n",
"\r\n",
"\t-g\t\tUse genome file to calculate empty regions.\r\n",
"\t\t\t- STRING.\r\n",
"\r\n",
"\t-empty\t\tReport empty regions (i.e., start/end intervals w/o\r\n",
"\t\t\tvalues in all files).\r\n",
"\t\t\t- Requires the '-g FILE' parameter.\r\n",
"\r\n",
"\t-filler TEXT\tUse TEXT when representing intervals having no value.\r\n",
"\t\t\t- Default is '0', but you can use 'N/A' or any text.\r\n",
"\r\n",
"\t-examples\tShow detailed usage examples.\r\n",
"\r\n"
]
}
],
"source": [
"!{bedtoolsDirectory}unionBedGraphs -h"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [],
"source": [
"#Create union BEDgraph from sorted files\n",
"#Include a header\n",
"#Use N/A when there is no data for a CpG in a sample\n",
"#Define sample IDs\n",
"#Use sorted bedgraphs\n",
"#Save output\n",
"!{bedtoolsDirectory}unionBedGraphs \\\n",
"-header \\\n",
"-filler N/A \\\n",
"-names 12M 13M 16F 19F 22F 23M 29F 31M 35F 36F 39F 3F 41F 44F 48M 50F 52F 53F 54F 59M 64M 6M 76F 77F 7M 9M \\\n",
"-i \\\n",
"*10x.SNPcorr.bedgraph \\\n",
"> union_10x.bedgraph"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"chrom\tstart\tend\t12M\t13M\t16F\t19F\t22F\t23M\t29F\t31M\t35F\t36F\t39F\t3F\t41F\t44F\t48M\t50F\t52F\t53F\t54F\t59M\t64M\t6M\t76F\t77F\t7M\t9M\n",
"NC_007175.2\t48\t50\t0.000000\t0.000000\t1.923077\t0.731452\t1.015228\t0.000000\t1.444623\t3.125000\t0.844511\t1.699182\t0.541339\t1.694915\t1.928375\t2.136076\t1.086957\t1.672640\t1.806240\t1.100917\t1.780694\t0.000000\t3.973510\t0.653595\t0.682057\t1.661475\t3.750000\t1.754386\n",
"NC_007175.2\t50\t52\t0.000000\t0.000000\t1.626016\t0.733855\t1.507937\t0.000000\t1.349325\t1.470588\t0.600462\t1.700880\t0.599908\t1.500000\t2.570694\t1.327434\t1.036269\t1.874311\t1.371951\t1.069218\t1.842105\t0.000000\t3.797468\t0.632911\t0.442478\t1.439539\t3.488372\t1.666667\n",
"NC_007175.2\t87\t89\t1.169591\t1.293103\t1.045857\t0.286907\t0.789771\t0.990099\t0.859599\t0.671141\t0.666349\t0.813008\t0.444115\t1.284875\t0.800915\t1.361796\t0.245700\t0.959596\t0.852273\t0.758853\t0.866927\t0.000000\t0.319489\t0.666667\t0.208008\t1.021477\t0.478469\t0.000000\n",
"NC_007175.2\t146\t148\t1.261830\t0.461894\t1.502146\t0.684369\t1.081187\t0.819672\t1.183206\t0.332226\t0.721028\t1.522344\t0.562023\t0.995025\t1.548541\t1.321760\t0.383142\t1.619645\t1.306458\t1.210914\t0.924855\t0.000000\t2.027027\t0.702988\t0.475325\t1.308017\t1.566580\t0.456621\n",
"NC_007175.2\t192\t194\t1.129944\t1.271186\t1.726908\t0.691776\t1.094563\t1.955990\t1.097734\t0.303951\t0.996997\t1.613626\t0.538915\t1.198820\t1.716501\t1.497326\t0.907029\t1.575555\t1.486346\t1.194200\t0.896287\t0.476190\t1.369863\t0.161031\t0.558659\t1.286383\t2.195122\t0.840336\n",
"NC_007175.2\t245\t247\t0.829876\t0.550964\t1.228250\t0.414110\t0.794148\t0.626959\t1.226456\t1.321586\t0.824253\t1.138753\t0.516834\t1.106095\t1.192146\t1.287830\t0.891530\t1.029454\t1.357658\t0.887178\t0.891720\t1.986755\t1.195219\t0.451467\t0.596787\t1.074455\t0.993377\t0.609756\n",
"NC_007175.2\t256\t258\t0.738007\t0.496278\t1.417467\t0.503960\t0.938518\t0.877193\t0.672202\t0.404858\t0.983946\t1.295966\t0.583658\t1.337793\t1.944793\t1.562191\t0.405954\t1.254246\t1.390498\t1.110242\t0.780142\t1.111111\t2.083333\t0.202429\t0.662633\t1.096523\t0.282486\t1.117318\n",
"NC_007175.2\t263\t265\t1.365188\t0.917431\t1.681034\t0.512963\t1.130356\t1.133144\t0.644183\t0.000000\t0.755699\t1.164596\t0.631720\t1.174831\t1.623572\t1.444653\t0.527704\t1.434933\t1.391432\t0.840336\t0.830341\t1.058201\t1.827243\t0.193424\t0.516615\t1.148459\t0.555556\t0.537634\n",
"NC_007175.2\t265\t267\t0.337838\t0.453515\t1.534527\t0.494302\t1.063255\t1.111111\t0.748783\t0.763359\t1.026895\t1.370074\t0.717227\t1.159363\t1.255230\t1.520208\t0.651890\t1.445724\t1.271340\t1.008005\t0.890869\t1.595745\t1.495017\t0.382409\t0.470719\t1.058348\t0.274725\t0.000000\n",
" 12951905 union_10x.bedgraph\n"
]
}
],
"source": [
"#Check output\n",
"!head union_10x.bedgraph\n",
"!wc -l union_10x.bedgraph"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 2b. Manipulate with `pandas`"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
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" 50 | \n",
" 1.923077 | \n",
" 0.731452 | \n",
" 1.015228 | \n",
" 1.444623 | \n",
" 0.844511 | \n",
" 1.699182 | \n",
" 0.541339 | \n",
" 1.694915 | \n",
" 1.928375 | \n",
" 2.136076 | \n",
" 1.672640 | \n",
" 1.806240 | \n",
" 1.100917 | \n",
" 1.780694 | \n",
" 0.682057 | \n",
" 1.661475 | \n",
"
\n",
" \n",
" | 1 | \n",
" NC_007175.2 | \n",
" 50 | \n",
" 52 | \n",
" 1.626016 | \n",
" 0.733855 | \n",
" 1.507937 | \n",
" 1.349325 | \n",
" 0.600462 | \n",
" 1.700880 | \n",
" 0.599908 | \n",
" 1.500000 | \n",
" 2.570694 | \n",
" 1.327434 | \n",
" 1.874311 | \n",
" 1.371951 | \n",
" 1.069218 | \n",
" 1.842105 | \n",
" 0.442478 | \n",
" 1.439539 | \n",
"
\n",
" \n",
" | 2 | \n",
" NC_007175.2 | \n",
" 87 | \n",
" 89 | \n",
" 1.045857 | \n",
" 0.286907 | \n",
" 0.789771 | \n",
" 0.859599 | \n",
" 0.666349 | \n",
" 0.813008 | \n",
" 0.444115 | \n",
" 1.284875 | \n",
" 0.800915 | \n",
" 1.361796 | \n",
" 0.959596 | \n",
" 0.852273 | \n",
" 0.758853 | \n",
" 0.866927 | \n",
" 0.208008 | \n",
" 1.021477 | \n",
"
\n",
" \n",
" | 3 | \n",
" NC_007175.2 | \n",
" 146 | \n",
" 148 | \n",
" 1.502146 | \n",
" 0.684369 | \n",
" 1.081187 | \n",
" 1.183206 | \n",
" 0.721028 | \n",
" 1.522344 | \n",
" 0.562023 | \n",
" 0.995025 | \n",
" 1.548541 | \n",
" 1.321760 | \n",
" 1.619645 | \n",
" 1.306458 | \n",
" 1.210914 | \n",
" 0.924855 | \n",
" 0.475325 | \n",
" 1.308017 | \n",
"
\n",
" \n",
" | 4 | \n",
" NC_007175.2 | \n",
" 192 | \n",
" 194 | \n",
" 1.726908 | \n",
" 0.691776 | \n",
" 1.094563 | \n",
" 1.097734 | \n",
" 0.996997 | \n",
" 1.613626 | \n",
" 0.538915 | \n",
" 1.198820 | \n",
" 1.716501 | \n",
" 1.497326 | \n",
" 1.575555 | \n",
" 1.486346 | \n",
" 1.194200 | \n",
" 0.896287 | \n",
" 0.558659 | \n",
" 1.286383 | \n",
"
\n",
" \n",
"
\n",
"
\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" chrom | \n",
" start | \n",
" end | \n",
" 16F | \n",
" 19F | \n",
" 22F | \n",
" 29F | \n",
" 35F | \n",
" 36F | \n",
" 39F | \n",
" ... | \n",
" 41F | \n",
" 44F | \n",
" 50F | \n",
" 52F | \n",
" 53F | \n",
" 54F | \n",
" 76F | \n",
" 77F | \n",
" total | \n",
" average | \n",
"
\n",
" \n",
" \n",
" \n",
" | 12678561 | \n",
" NC_035789.1 | \n",
" 32649654 | \n",
" 32649656 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678562 | \n",
" NC_035789.1 | \n",
" 32649732 | \n",
" 32649734 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678563 | \n",
" NC_035789.1 | \n",
" 32649736 | \n",
" 32649738 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678564 | \n",
" NC_035789.1 | \n",
" 32649799 | \n",
" 32649801 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678565 | \n",
" NC_035789.1 | \n",
" 32649876 | \n",
" 32649878 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678566 | \n",
" NC_035789.1 | \n",
" 32649885 | \n",
" 32649887 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678567 | \n",
" NC_035789.1 | \n",
" 32649895 | \n",
" 32649897 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678568 | \n",
" NC_035789.1 | \n",
" 32649930 | \n",
" 32649932 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678569 | \n",
" NC_035789.1 | \n",
" 32649933 | \n",
" 32649935 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 12678570 | \n",
" NC_035789.1 | \n",
" 32649966 | \n",
" 32649968 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" ... | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
"
\n",
"
10 rows × 21 columns
\n",
"
\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" chrom | \n",
" start | \n",
" end | \n",
" 12M | \n",
" 13M | \n",
" 23M | \n",
" 31M | \n",
" 48M | \n",
" 59M | \n",
" 64M | \n",
" 6M | \n",
" 7M | \n",
" 9M | \n",
"
\n",
" \n",
" \n",
" \n",
" | 0 | \n",
" NC_007175.2 | \n",
" 48 | \n",
" 50 | \n",
" 0.000000 | \n",
" 0.000000 | \n",
" 0.000000 | \n",
" 3.125000 | \n",
" 1.086957 | \n",
" 0.00000 | \n",
" 3.973510 | \n",
" 0.653595 | \n",
" 3.750000 | \n",
" 1.754386 | \n",
"
\n",
" \n",
" | 1 | \n",
" NC_007175.2 | \n",
" 50 | \n",
" 52 | \n",
" 0.000000 | \n",
" 0.000000 | \n",
" 0.000000 | \n",
" 1.470588 | \n",
" 1.036269 | \n",
" 0.00000 | \n",
" 3.797468 | \n",
" 0.632911 | \n",
" 3.488372 | \n",
" 1.666667 | \n",
"
\n",
" \n",
" | 2 | \n",
" NC_007175.2 | \n",
" 87 | \n",
" 89 | \n",
" 1.169591 | \n",
" 1.293103 | \n",
" 0.990099 | \n",
" 0.671141 | \n",
" 0.245700 | \n",
" 0.00000 | \n",
" 0.319489 | \n",
" 0.666667 | \n",
" 0.478469 | \n",
" 0.000000 | \n",
"
\n",
" \n",
" | 3 | \n",
" NC_007175.2 | \n",
" 146 | \n",
" 148 | \n",
" 1.261830 | \n",
" 0.461894 | \n",
" 0.819672 | \n",
" 0.332226 | \n",
" 0.383142 | \n",
" 0.00000 | \n",
" 2.027027 | \n",
" 0.702988 | \n",
" 1.566580 | \n",
" 0.456621 | \n",
"
\n",
" \n",
" | 4 | \n",
" NC_007175.2 | \n",
" 192 | \n",
" 194 | \n",
" 1.129944 | \n",
" 1.271186 | \n",
" 1.955990 | \n",
" 0.303951 | \n",
" 0.907029 | \n",
" 0.47619 | \n",
" 1.369863 | \n",
" 0.161031 | \n",
" 2.195122 | \n",
" 0.840336 | \n",
"
\n",
" \n",
"
\n",
"
\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" chrom | \n",
" start | \n",
" end | \n",
" 12M | \n",
" 13M | \n",
" 23M | \n",
" 31M | \n",
" 48M | \n",
" 59M | \n",
" 64M | \n",
" 6M | \n",
" 7M | \n",
" 9M | \n",
" total | \n",
" average | \n",
"
\n",
" \n",
" \n",
" \n",
" | 11991486 | \n",
" NC_035789.1 | \n",
" 32649654 | \n",
" 32649656 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991487 | \n",
" NC_035789.1 | \n",
" 32649732 | \n",
" 32649734 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991488 | \n",
" NC_035789.1 | \n",
" 32649736 | \n",
" 32649738 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991489 | \n",
" NC_035789.1 | \n",
" 32649799 | \n",
" 32649801 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991490 | \n",
" NC_035789.1 | \n",
" 32649876 | \n",
" 32649878 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991491 | \n",
" NC_035789.1 | \n",
" 32649885 | \n",
" 32649887 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991492 | \n",
" NC_035789.1 | \n",
" 32649895 | \n",
" 32649897 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991493 | \n",
" NC_035789.1 | \n",
" 32649930 | \n",
" 32649932 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991494 | \n",
" NC_035789.1 | \n",
" 32649933 | \n",
" 32649935 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
" | 11991495 | \n",
" NC_035789.1 | \n",
" 32649966 | \n",
" 32649968 | \n",
" NaN | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
" 0.0 | \n",
" 0.0 | \n",
"
\n",
" \n",
"
\n",
"