sam.md

samtools extras

To play around with a few samtools commands, first change directories into the directory containing all BAM files.

$ cd ~/unix_workshop/rnaseq/results/STAR/bams

Write only mapped reads to file (filter out unmapped reads)

$ samtools view -b -h -F 4 Mov10_oe_1_Aligned.sortedByCoord.out.bam > Mov10_oe_1_Aligned.onlyAligned.bam

Create a FASTQ file containing only mapped reads

$ bamtofastq -o Mov10_oe_1_Mapped.fastq --no-unaligned Mov10_oe_1_Aligned.onlyMapped.bam

Index BAM file

$ samtools index Mov10_oe_1_Aligned.sortedByCoord.out.bam

Extract reads from a specific region of the chromosome

$samtools view Mov10_oe_1_Aligned.sortedByCoord.out.bam chr1:200000-500000

Randomly subsample half of the reads into a new BAM file

$ samtools view -s 0.5 -b Mov10_oe_1_Aligned.sortedByCoord.out.bam > Mov10_oe_1_subsample.bam

Simple stats for alignment file

$ samtools flagstat Mov10_oe_1_Aligned.sortedByCoord.out.bam

Visualizing mismatches

$ samtools view -h Mov10_oe_1_Aligned.sortedByCoord.out.bam | head -n 5 | samtools fillmd -e - ~/unix_workshop/rnaseq/reference_data/chr1.fa