sorted bam file

Question

[evelyn]

Hi,

I am trying to calculate the sequencing depth for sorted bam files made using bowtie. I am using:

samtools depth bowtie_sorted.bam |  awk '{sum+=$3} END { print "Average = ",sum/NR}'

I have many sorted bam files and I want to calculate the depth for all using one array job rather than calculating for all files individually. Can anyone help writing such an array? Thanks!

[WouterDeCoster]

Your thread is about calculating the depth of bam files. But your title is sorted bam file? Please select a more descriptive title, and use sensible tags.

Answer 1

[ATpoint]

ls *.bam | parallel -j <NumberOfParallelJobs> "samtools flagstat {} > {.}.flagstat"

This gives a complete overview over the number of mapped/unmapped reads etc. Alternatively, index the files and use samtools idxstats followed by summing up the reads of all chromosomes.

[evelyn]

I want to calculate the sequencing depth.