This notebook is a continuation of using Bismark (Krueger and Andrews 2011) to perform methylation analysis. This step will perform methylation extraction.
Results will be summarized by MultiQC (Ewels et al. 2016).
This notebook relies on deduplicated BAMs generated by 02.10-bismark-deduplication.Rmd.
*.CpG_report.merged_CpG_evidence.cov.gz: CpG position and counts merged from all strands. Generated by coverage2cytosine.
*.deduplicated.bedGraph.gz: Bedgraph file with CpG loci and percent methylation.
*.deduplicated.bedGraph.gz.bismark.zero.cov: Extension of *deduplicated.bedGraph.gz which includes two additional columns, count methylated and count unmethylated, in that order.
*.deduplicated.bismark.cov.gz: 1-based counting version of *.deduplicated.bedGraph.gz.bismark.zero.cov. E.g. loci are at 49 49, instead of 48 49.
*.deduplicated.CpG_report.txt.gz: Report on all CpGs. <chromosome> <0-based start> <methylation status, +/-> <count_methyldated> <CG> <trinucleotide_context>
*.deduplicated.cytosine_context_summary.txt: Cytosine context summary. See file headers for info.
*.deduplicated.M-bias.txt: Methylation bias table. See file headers for info.
*.deduplicated_splitting_report.txt: Summary methylation report in a human-readable format.
CH*.deduplicated.txt.gz: Strand-specific methylation status for each read in CHH or CHG context.
CpG*.deduplicated.txt.gz: Strand-specific methylation status for each read in CpG context.
multiqc_report.html: A summary report of the alignment results generated by MultiQC, in HTML format.
Due to the large file sizes of most of the output files, these cannot be hosted in the ceasmallr GitHub repo. As such these files are available for download here:
This allows usage of Bash variables across R Markdown chunks.
{
echo "#### Assign Variables ####"
echo ""
echo "# Data directories"
echo 'export repo_dir=/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr'
echo 'export output_dir_top=${repo_dir}/output/02.20-bismark-methylation-extraction'
echo 'export deduplication_dir="${repo_dir}/output/02.10-bismark-deduplication"'
echo 'export genome_dir="${repo_dir}/data/Cvirginica_v300/"'
echo ""
echo "# Paths to programs"
echo 'export programs_dir="/home/shared"'
echo 'export bismark_dir="${programs_dir}/Bismark-0.24.0"'
echo 'export bowtie2_dir="${programs_dir}/bowtie2-2.4.4-linux-x86_64"'
echo 'export multiqc="/home/sam/programs/mambaforge/bin/multiqc"'
echo 'export samtools_dir="${programs_dir}/samtools-1.12"'
echo ""
echo "# Set number of CPUs to use"
echo 'export threads=40'
echo "# Print formatting"
echo 'export line="--------------------------------------------------------"'
echo ""
} > .bashvars
cat .bashvars#### Assign Variables ####
# Data directories
export repo_dir=/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr
export output_dir_top=${repo_dir}/output/02.20-bismark-methylation-extraction
export deduplication_dir="${repo_dir}/output/02.10-bismark-deduplication"
export genome_dir="${repo_dir}/data/Cvirginica_v300/"
# Paths to programs
export programs_dir="/home/shared"
export bismark_dir="${programs_dir}/Bismark-0.24.0"
export bowtie2_dir="${programs_dir}/bowtie2-2.4.4-linux-x86_64"
export multiqc="/home/sam/programs/mambaforge/bin/multiqc"
export samtools_dir="${programs_dir}/samtools-1.12"
# Set number of CPUs to use
export threads=40
# Print formatting
export line="--------------------------------------------------------"# Load bash variables into memory
source .bashvars
cd "${deduplication_dir}"
${bismark_dir}/bismark_methylation_extractor \
--bedGraph \
--counts \
--scaffolds \
--parallel 10 \
--output_dir ${output_dir_top} \
--samtools_path ${samtools_dir} \
--gzip \
--paired-end \
--comprehensive \
--merge_non_CpG \
--zero_based \
--buffer_size 75% \
--cytosine_report \
--genome_folder ${genome_dir} \
*deduplicated.bam# Load bash variables into memory
source .bashvars
cd "${output_dir_top}"
find *deduplicated.bismark.cov.gz \
| xargs basename -s _bismark_bt2_pe.deduplicated.bismark.cov.gz \
| xargs -I{} ${bismark_dir}/coverage2cytosine \
--genome_folder ${genome_dir} \
-o {} \
--merge_CpG \
--zero_based \
--gzip \
{}_bismark_bt2_pe.deduplicated.bismark.cov.gz
Glance at output file formats, using CF01-CM01-Zygote files as example.
# Load bash variables into memory
source .bashvars
cd "${output_dir_top}"
for file in *CF01-CM01-Zygote*; do
if [[ -f "$file" ]]; then
if [[ "$file" == *.gz ]]; then
echo "<===== $file ====>"
echo ""
zcat "$file" | head | column -t -s $'\t'
echo ""
echo "${line}"
echo ""
else
echo "<===== $file ====>"
echo ""
echo "$file"
head "$file" | column -t -s $'\t'
echo ""
echo "${line}"
echo ""
fi
fi
done
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bedGraph.gz ====>
track type=bedGraph
NC_007175.2 48 49 2.08333333333333
NC_007175.2 49 50 0
NC_007175.2 50 51 1.92307692307692
NC_007175.2 51 52 0
NC_007175.2 87 88 0
NC_007175.2 88 89 0
NC_007175.2 146 147 0
NC_007175.2 147 148 1.75438596491228
NC_007175.2 148 149 0
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov ====>
CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov
NC_007175.2 48 49 2.08333333333333 1 47
NC_007175.2 49 50 0 0 2
NC_007175.2 50 51 1.92307692307692 1 51
NC_007175.2 51 52 0 0 1
NC_007175.2 87 88 0 0 104
NC_007175.2 88 89 0 0 33
NC_007175.2 146 147 0 0 116
NC_007175.2 147 148 1.75438596491228 1 56
NC_007175.2 148 149 0 0 1
NC_007175.2 192 193 0 0 51
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bismark.cov.gz ====>
NC_007175.2 49 49 2.08333333333333 1 47
NC_007175.2 50 50 0 0 2
NC_007175.2 51 51 1.92307692307692 1 51
NC_007175.2 52 52 0 0 1
NC_007175.2 88 88 0 0 104
NC_007175.2 89 89 0 0 33
NC_007175.2 147 147 0 0 116
NC_007175.2 148 148 1.75438596491228 1 56
NC_007175.2 149 149 0 0 1
NC_007175.2 193 193 0 0 51
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.CpG_report.txt.gz ====>
NC_007175.2 48 + 1 47 CG CGC
NC_007175.2 49 - 0 2 CG CGA
NC_007175.2 50 + 1 51 CG CGG
NC_007175.2 51 - 0 1 CG CGC
NC_007175.2 87 + 0 104 CG CGT
NC_007175.2 88 - 0 33 CG CGT
NC_007175.2 146 + 0 116 CG CGG
NC_007175.2 147 - 1 56 CG CGA
NC_007175.2 192 + 0 51 CG CGC
NC_007175.2 193 - 0 39 CG CGA
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt ====>
CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt
upstream C-context full context count methylated count unmethylated percent methylation
A CAA ACAA 66 446 12.89
C CAA CCAA 66 479 12.11
G CAA GCAA 19 198 8.76
T CAA TCAA 59 526 10.09
A CAC ACAC 16 118 11.94
C CAC CCAC 7 69 9.21
G CAC GCAC 9 38 19.15
T CAC TCAC 15 120 11.11
A CAG ACAG 142 1235 10.31
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.M-bias.txt ====>
CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.M-bias.txt
CpG context (R1)
================
position count methylated count unmethylated % methylation coverage
1 9383 45046 17.24 54429
2 9270 45432 16.95 54702
3 9184 45622 16.76 54806
4 9457 45750 17.13 55207
5 10083 48122 17.32 58205
6 10548 48157 17.97 58705
7 10617 48528 17.95 59145
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated_splitting_report.txt ====>
CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated_splitting_report.txt
CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bam
Parameters used to extract methylation information:
Bismark Extractor Version: v0.24.0
Bismark result file: paired-end (SAM format)
Output specified: comprehensive
No overlapping methylation calls specified
Methylation in CHG and CHH context will be merged into "non-CpG context" output
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED.CpG_report.merged_CpG_evidence.cov.gz ====>
NC_007175.2 48 50 2.000000 1 49
NC_007175.2 50 52 1.886792 1 52
NC_007175.2 87 89 0.000000 0 137
NC_007175.2 146 148 0.578035 1 172
NC_007175.2 192 194 0.000000 0 90
NC_007175.2 245 247 2.898551 2 67
NC_007175.2 256 258 4.166667 5 115
NC_007175.2 263 265 0.000000 0 155
NC_007175.2 265 267 1.142857 2 173
NC_007175.2 331 333 0.546448 1 182
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED.CpG_report.txt.gz ====>
NC_007175.2 48 + 1 47 CG CGC
NC_007175.2 49 - 0 2 CG CGA
NC_007175.2 50 + 1 51 CG CGG
NC_007175.2 51 - 0 1 CG CGC
NC_007175.2 87 + 0 104 CG CGT
NC_007175.2 88 - 0 33 CG CGT
NC_007175.2 146 + 0 116 CG CGG
NC_007175.2 147 - 1 56 CG CGA
NC_007175.2 192 + 0 51 CG CGC
NC_007175.2 193 - 0 39 CG CGA
--------------------------------------------------------
<===== CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED.cytosine_context_summary.txt ====>
CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED.cytosine_context_summary.txt
upstream C-context full context count methylated count unmethylated percent methylation
A CAA ACAA 66 446 12.89
C CAA CCAA 66 479 12.11
G CAA GCAA 19 198 8.76
T CAA TCAA 59 526 10.09
A CAC ACAC 16 118 11.94
C CAC CCAC 7 69 9.21
G CAC GCAC 9 38 19.15
T CAC TCAC 15 120 11.11
A CAG ACAG 142 1235 10.31
--------------------------------------------------------
<===== CpG_context_CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.txt.gz ====>
Bismark methylation extractor version v0.24.0
GWNJ-1012:512:GW210315000:4:1101:21884:1094_1:N:0:TTATAACC+TCGATATC - NC_035785.1 24407680 z
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653438 z
GWNJ-1012:512:GW210315000:4:1101:20699:1141_1:N:0:TTATAACC+TCGATATC - NC_035788.1 57095043 z
GWNJ-1012:512:GW210315000:4:1101:20699:1141_1:N:0:TTATAACC+TCGATATC - NC_035788.1 57095087 z
GWNJ-1012:512:GW210315000:4:1101:20699:1141_1:N:0:TTATAACC+TCGATATC - NC_035788.1 57095119 z
GWNJ-1012:512:GW210315000:4:1101:20699:1141_1:N:0:TTATAACC+TCGATATC - NC_035788.1 57095138 z
GWNJ-1012:512:GW210315000:4:1101:9372:1595_1:N:0:TTATAACC+TCGATATC + NC_035781.1 2018694 Z
GWNJ-1012:512:GW210315000:4:1101:15402:1642_1:N:0:TTATAACC+TCGATATC + NC_035783.1 49860452 Z
GWNJ-1012:512:GW210315000:4:1101:9372:1595_1:N:0:TTATAACC+TCGATATC + NC_035781.1 2018682 Z
--------------------------------------------------------
<===== Non_CpG_context_CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.txt.gz ====>
Bismark methylation extractor version v0.24.0
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653467 x
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653466 h
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653465 h
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653464 h
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653461 x
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653455 h
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653454 h
GWNJ-1012:512:GW210315000:4:1101:11776:1219_1:N:0:TTATAACC+TCGATATC - NC_035780.1 32653450 h
GWNJ-1012:512:GW210315000:4:1101:20699:1141_1:N:0:TTATAACC+TCGATATC + NC_035788.1 57095003 X
--------------------------------------------------------# Load bash variables into memory
source .bashvars
cd "${output_dir_top}"
ls -lhtotal 93G
-rw-r--r-- 1 sam sam 21M Nov 26 11:17 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bedGraph.gz
-rw-r--r-- 1 sam sam 124M Nov 26 11:17 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov
-rw-r--r-- 1 sam sam 18M Nov 26 11:17 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bismark.cov.gz
-rw-r--r-- 1 sam sam 107M Nov 26 11:27 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.7K Dec 4 12:17 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 20K Dec 4 12:17 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.M-bias.txt
-rw-r--r-- 1 sam sam 926 Dec 4 12:17 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated_splitting_report.txt
-rw-r--r-- 1 sam sam 21M Dec 4 12:17 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED.CpG_report.merged_CpG_evidence.cov.gz
-rw-r--r-- 1 sam sam 107M Nov 27 07:59 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.7K Dec 4 12:17 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 90M Nov 26 11:43 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz
-rw-r--r-- 1 sam sam 551M Nov 26 11:43 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov
-rw-r--r-- 1 sam sam 89M Nov 26 11:43 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
-rw-r--r-- 1 sam sam 126M Nov 26 11:54 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 23K Dec 4 12:17 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.M-bias.txt
-rw-r--r-- 1 sam sam 928 Dec 4 12:17 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated_splitting_report.txt
-rw-r--r-- 1 sam sam 72M Dec 4 12:17 CF01-CM02-Larvae_R1_001.fastp-trim.CpG_report.merged_CpG_evidence.cov.gz
-rw-r--r-- 1 sam sam 126M Nov 27 08:11 CF01-CM02-Larvae_R1_001.fastp-trim.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF01-CM02-Larvae_R1_001.fastp-trim.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 44M Nov 26 12:00 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz
-rw-r--r-- 1 sam sam 263M Nov 26 12:00 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov
-rw-r--r-- 1 sam sam 41M Nov 26 12:00 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
-rw-r--r-- 1 sam sam 113M Nov 26 12:12 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 21K Dec 4 12:17 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.M-bias.txt
-rw-r--r-- 1 sam sam 926 Dec 4 12:17 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated_splitting_report.txt
-rw-r--r-- 1 sam sam 41M Dec 4 12:17 CF02-CM02-Zygote_R1_001.fastp-trim.CpG_report.merged_CpG_evidence.cov.gz
-rw-r--r-- 1 sam sam 113M Nov 27 08:22 CF02-CM02-Zygote_R1_001.fastp-trim.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF02-CM02-Zygote_R1_001.fastp-trim.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 65M Nov 26 12:20 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz
-rw-r--r-- 1 sam sam 395M Nov 26 12:20 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov
-rw-r--r-- 1 sam sam 61M Nov 26 12:20 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
-rw-r--r-- 1 sam sam 118M Nov 26 12:32 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 22K Dec 4 12:17 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.M-bias.txt
-rw-r--r-- 1 sam sam 925 Dec 4 12:17 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated_splitting_report.txt
-rw-r--r-- 1 sam sam 57M Dec 4 12:17 CF03-CM03-Zygote_R1_001.fastp-trim.CpG_report.merged_CpG_evidence.cov.gz
-rw-r--r-- 1 sam sam 118M Nov 27 08:33 CF03-CM03-Zygote_R1_001.fastp-trim.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF03-CM03-Zygote_R1_001.fastp-trim.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 85M Nov 26 12:45 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz
-rw-r--r-- 1 sam sam 528M Nov 26 12:45 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov
-rw-r--r-- 1 sam sam 83M Nov 26 12:45 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
-rw-r--r-- 1 sam sam 123M Nov 26 12:57 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 23K Dec 4 12:17 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.M-bias.txt
-rw-r--r-- 1 sam sam 927 Dec 4 12:17 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated_splitting_report.txt
-rw-r--r-- 1 sam sam 69M Dec 4 12:17 CF03-CM04-Larvae_R1_001.fastp-trim.CpG_report.merged_CpG_evidence.cov.gz
-rw-r--r-- 1 sam sam 123M Nov 27 08:45 CF03-CM04-Larvae_R1_001.fastp-trim.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF03-CM04-Larvae_R1_001.fastp-trim.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 90M Nov 26 13:12 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz
-rw-r--r-- 1 sam sam 551M Nov 26 13:12 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov
-rw-r--r-- 1 sam sam 88M Nov 26 13:12 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
-rw-r--r-- 1 sam sam 125M Nov 26 13:23 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 23K Dec 4 12:17 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.M-bias.txt
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-rw-r--r-- 1 sam sam 72M Dec 4 12:17 EF08-EM03-Larvae_R1_001.fastp-trim.CpG_report.merged_CpG_evidence.cov.gz
-rw-r--r-- 1 sam sam 125M Nov 27 13:46 EF08-EM03-Larvae_R1_001.fastp-trim.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 EF08-EM03-Larvae_R1_001.fastp-trim.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 84M Nov 26 22:31 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz
-rw-r--r-- 1 sam sam 517M Nov 26 22:31 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bedGraph.gz.bismark.zero.cov
-rw-r--r-- 1 sam sam 82M Nov 26 22:31 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
-rw-r--r-- 1 sam sam 124M Nov 26 22:43 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.cytosine_context_summary.txt
-rw-r--r-- 1 sam sam 23K Dec 4 12:17 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.M-bias.txt
-rw-r--r-- 1 sam sam 928 Dec 4 12:17 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated_splitting_report.txt
-rw-r--r-- 1 sam sam 68M Dec 4 12:17 EF08-EM04-Larvae_R1_001.fastp-trim.CpG_report.merged_CpG_evidence.cov.gz
-rw-r--r-- 1 sam sam 124M Nov 27 13:57 EF08-EM04-Larvae_R1_001.fastp-trim.CpG_report.txt.gz
-rw-r--r-- 1 sam sam 1.8K Dec 4 12:17 EF08-EM04-Larvae_R1_001.fastp-trim.cytosine_context_summary.txt
drwxr-xr-x 2 sam sam 4.0K Dec 4 12:17 multiqc_data
-rw-r--r-- 1 sam sam 1.2M Dec 4 12:17 multiqc_report.html
-rw-r--r-- 1 sam sam 191M Nov 26 11:16 Non_CpG_context_CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.6G Nov 26 11:37 Non_CpG_context_CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 890M Nov 26 11:59 Non_CpG_context_CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 1.3G Nov 26 12:18 Non_CpG_context_CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.2G Nov 26 12:41 Non_CpG_context_CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.4G Nov 26 13:07 Non_CpG_context_CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 1.6G Nov 26 13:30 Non_CpG_context_CF04-CM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 3.4G Nov 26 13:58 Non_CpG_context_CF05-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 1.9G Nov 26 14:25 Non_CpG_context_CF05-CM05-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 1.6G Nov 26 14:47 Non_CpG_context_CF06-CM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 1.4G Nov 26 15:07 Non_CpG_context_CF06-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 992M Nov 26 15:25 Non_CpG_context_CF07-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 970M Nov 26 15:42 Non_CpG_context_CF08-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 29M Nov 26 15:55 Non_CpG_context_CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 27M Nov 26 16:05 Non_CpG_context_CF08-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 1.5G Nov 26 16:21 Non_CpG_context_EF01-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 1.6G Nov 26 16:42 Non_CpG_context_EF02-EM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 904M Nov 26 17:01 Non_CpG_context_EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.3G Nov 26 17:23 Non_CpG_context_EF03-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.4G Nov 26 17:49 Non_CpG_context_EF03-EM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 485M Nov 26 18:08 Non_CpG_context_EF04-EM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 3.1G Nov 26 18:32 Non_CpG_context_EF04-EM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 1.9G Nov 26 18:58 Non_CpG_context_EF05-EM01-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 275M Nov 26 19:14 Non_CpG_context_EF05-EM05-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 3.4G Nov 26 19:39 Non_CpG_context_EF05-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 3.1G Nov 26 20:10 Non_CpG_context_EF06-EM01-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.3G Nov 26 20:38 Non_CpG_context_EF06-EM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 550M Nov 26 20:57 Non_CpG_context_EF06-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 653M Nov 26 21:12 Non_CpG_context_EF07-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.4G Nov 26 21:33 Non_CpG_context_EF07-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.7G Nov 26 22:01 Non_CpG_context_EF08-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz
-rw-r--r-- 1 sam sam 2.1G Nov 26 22:27 Non_CpG_context_EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.txt.gz# Load bash variables into memory
source .bashvars
cd "${output_dir_top}"
for file in *; do
if [ "${file}" != "checksums.md5" ]; then
md5sum "${file}" >> checksums.md5
fi
done# Load bash variables into memory
source .bashvars
cd "${output_dir_top}"
${multiqc} .