7.Samtools to select reads that are mapped

1. Samtools introduction:

1.1: Purpose function:

Purpose:
Use SAMtools to convert SAM files to BAM files, sort, and index them
See: https://blog.csdn.net/xiaomotong123/article/details/106504192/
Function

1.2: Installation:

conda install -y samtools

2.sam to bam

Samtools View-@8-s 2d.sam-o 2d.bam (single Sam file) (Batch processing) INDEX=./bwa_index/2019-nCoV.fasta for i in $(ls *.sam) do i=${i/.sam/} samtools view -@ 8 -S $i.sam -1b -o $i.bam done

3.Samtools sort

Samtools sort-@8-L 5-o 2d.bam. Sort 2d.bam (single BAM) samtools sort -@ 8 -l 5 -o {$i}.bam.sort {$i}.bam samtools sort -@ 8 -l 5 -n -o P10.bam.sort XGRNAMIX1-10-N-RNA_L3.bam -@ Number of threads - L compression level - O output form -n sorted by read Name

The BAM file sort gets smaller:
BAM file is a compressed binary file, after sorting the contents of the file, similar contents are arranged together, so the compression ratio of the file is improved, so the BAM file after sorting becomes smaller, and the corresponding SAM file is a plain text file.
Sorting the SAM file will not change the file size. Reads with no alignment are placed at the end of the BAM file after samTools sorts it.

4.Samtools index

samtools index -@ 8 2nd.bam.sort 2nd.bam.index samtools index -@ 8 {$i}.bam.sort {$i}.bam.index

5.Samtools flagstat

samtools flagstat -@ 8 2nd.bam.sort samtools flagstat -@ 8 {$i}.bam.sort

6. Compose scripts

#! /bin/bash # Concatenates the view, sort, and index commands of SamTools For I in stores file names do samtools view -@ 8 -S /$i.sam -1b -o /$i.bam samtools sort -@ 8 -l 5 -o /$i.bam.sort /aligned/$i.bam samtools index -@ 8 /$i.bam.sort /$i.bam.index done

7. Interpretation of SAM-BAM-sort-index-Flagstat results

7.1: Sam, BAM, bam. Sort file size

7.2: Flagstata results (note the results in red)