How to filter a .bam file and keep the subjects

[leorippel]

Hello All,

I have multiple alignments generated to DEG analysis. I know that grep for unaligned reads is not trust and the best way is the -f4 flag. But here what I want is the contigs with no alignment with those reds from specific libraries.

I already have the counts matrices and I can grep those sequences from the matrix, but I want to do a sanity check .


Thank's in advanced.

[mastal]

Samtools idxstats should give you a list of how many reads aligned to each of the contigs in your reference genome, i.e. the sequences that are listed in the sam/bam headers.