htseq for specific features

Question

[simonjean434]

Hello,

I have a bed file with genomic ranges. I would like to use htseq to count reads from my bam file that mapped to these particular regions.

Could you please let me know how I can do that with htseq ?

Thanks J

[GenoMax]

Why not use bedtools instead?

[GouthamAtla]

or ( along with beddtools ) you could use featureCounts instead of htseq-count unless there are overlapping ambiguous regions.