Small RNA sequence, how to calculate read counts? What's the criterion? Is there soft

[vivi-Jasmine]

After alignment small RNA sequence to the reference genome using bowtie. I got SAM file, then how to calculate read counts? What's the criterion? Is there software to do this work?

[ymc]

htseq can give you the counts

[vivi-Jasmine]

htseq can give you the counts

Thank you for your reply, but htseq script showed that it mainly process RNA-seq data, but not small RNA data?

[GenoMax]

featureCounts (and htseq-count) count features based on the annotation file you provide. Provide locations of the smallRNA's you are interested in (GTF format) to get the counts you want.

[vivi-Jasmine]

featureCounts (and htseq-count) count features based on the annotation file you provide. Provide locations of the smallRNA's you are interested in (GTF format) to get the counts you want.

Thank you very much, you solved my perplexity.

[vivi-Jasmine]

featureCounts (and htseq-count) count features based on the annotation file you provide. Provide locations of the smallRNA's you are interested in (GTF format) to get the counts you want.

Hi GenoMax,
I analysis small RNA of switchgrass. It has not GTF file of small RNA. The reference genome of switchgrass has not assemble completely yet. In this situation, is there any other software I can use to caculate read counts? Thank you very much.

[GenoMax]

Sounds like you are doing your alignments against the genome (incomplete assembly)?

See if this site can help: http://smallrna.udel.edu/index.php