how to reserve the U&P reads of alignment bam file?

[Yuzhang0102]

Hi Mike, I used ShortStack4 aligned my sRNA reads to genome, and I got the alignment_details.tsv and many bam files. And I have annotation file predicted by other softwares, so I want to call counts using bam and annotation file by featureCounts.

But I need to filter reads that were labelled "R","H","N" in alignment_details.tsv, how can i filter them from bam files?

Thanks a lot.