Small RNA Read Counts

[WHP]

New to NGS data, currently analyzing small RNA seq data with emphasis on piRNAs, looking to eventually do differential expression analysis. I have my reads aligned, but now a little unsure of how best to go about getting total read counts for the areas of the genome I am interested in. I have ~500 genomic coordinates for regions of interest which should be areas of piRNA production.

I'm thinking of using bedtools to get a count of alignments which overlap with my ~500 regions. Is there a better way to do this? Suggestions and useful commands/parameters/programs very welcome.

Cheers

[Bukowski]

htseq-count is often used for this.

http://www-huber.embl.de/users/anders/HTSeq/doc/count.html

[vivi-Jasmine]

New to NGS data, currently analyzing small RNA seq data with emphasis on piRNAs, looking to eventually do differential expression analysis. I have my reads aligned, but now a little unsure of how best to go about getting total read counts for the areas of the genome I am interested in. I have ~500 genomic coordinates for regions of interest which should be areas of piRNA production.

I'm thinking of using bedtools to get a count of alignments which overlap with my ~500 regions. Is there a better way to do this? Suggestions and useful commands/parameters/programs very welcome.

Cheers

Hi, did you resolve your problem? I come across the same question.