---
title: "06-alignments"
author: "Olivia Cattau"
date: '2023-05-02'
output: html_document
---
#Introduction/Task 1
This week, we will consider a different way of looking at the relatedness of genetic information: single nucleotide polymorphisms (SNPs). SNPs are used to describe population variation or phylogenetic relationships. A first step in this is aligning sequence reads to look for variation.


## SAM and BAM files
SAM (Sequence Alignment/Map) and BAM (Binary Alignment/Map) are two file formats used to store aligned sequencing data. Both formats are designed to store read alignments from high-throughput sequencing experiments to a reference genome. 

## SAMtools
Samtools is a software package designed for manipulating and analyzing high-throughput sequencing data, specifically SAM (Sequence Alignment/Map) and BAM (Binary Alignment/Map) files. 


#Download alignmnet data
```{r, engine='bash'}         
cd ../data
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai
```

```{r, engine='bash'}         
cd ../data
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/data/Cvirg-genome/GCF_002022765.2_C_virginica-3.0_genomic.fa
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/data/Cvirg-genome/GCF_002022765.2_C_virginica-3.0_genomic.fa.fai
```

##View TVIEW
### Run in command line
/home/shared/samtools-1.12/samtools tview \
/home/olivia/gitrepos/olivia-classwork/assignments/code/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam \
/home/olivia/gitrepos/olivia-classwork/assignments/code/GCF_002022765.2_C_virginica-3.0_genomic.fa

#Task 2
##Aligning WGS data and visualizing in IGV

```{r, engine='bash'}
cd ../data
curl -O https://owl.fish.washington.edu/nightingales/C_gigas/F143n08_R2_001.fastq.gz
curl -O https://owl.fish.washington.edu/nightingales/C_gigas/F143n08_R1_001.fastq.gz
```

```{r, engine='bash'}
cd ../data
curl -O https://gannet.fish.washington.edu/panopea/Cg-roslin/cgigas_uk_roslin_v1_genomic-mito.fa
curl -O https://gannet.fish.washington.edu/panopea/Cg-roslin/cgigas_uk_roslin_v1_genomic-mito.fa.fai
curl -O https://gannet.fish.washington.edu/panopea/Cg-roslin/GCF_902806645.1_cgigas_uk_roslin_v1_genomic-mito.gtf
```


## Alignment
```{r, engine='bash'}
/home/shared/hisat2-2.2.1/hisat2-build \
-f /home/olivia/gitrepos/olivia-classwork/assignments/code/cgigas_uk_roslin_v1_genomic-mito.fa \
/home/olivia/gitrepos/olivia-classwork/assignments/output/cgigas_uk_roslin_v1_genomic-mito.index
```

```{r, engine='bash'}
/home/shared/hisat2-2.2.1/hisat2 \
-x /home/olivia/gitrepos/olivia-classwork/assignments/output/cgigas_uk_roslin_v1_genomic-mito.index \
-p 4 \
-1 /home/olivia/gitrepos/olivia-classwork/assignments/code/F143n08_R1_001.fastq.gz \
-2 /home/olivia/gitrepos/olivia-classwork/assignments/code/F143n08_R2_001.fastq.gz \
-S /home/olivia/gitrepos/olivia-classwork/assignments/output/F143_cgigas.sam
```

##take a look
```{r, engine='bash'}
tail -1 ../output/F143_cgigas.sam
```