Map Smallrna-Seq On Mirna

Question

[Nicolas Rosewick]

Hi,

I've smallRNA-seq data and want to count the number of read for each miRNA. I'm studying samples from a non-well annotated species so I've to use mirbases sequences from a related species. My idea is to use bowtie to map the reads on miRNA mature sequences. But is bowtie a good idea to align small reads on small sequences ? Anyone has an another idea ?

Thanks

N.

Answer 1

[Mike Axtell]

See How can I accurately identify miRNA sequences from small RNA seq results

Short answer: For tallying exact matches to known mature miRNAs, a simple homemade string-matching script will suffice. But to also capture isomirs / processing variants / non-templated tailed species in your counts, an aligner is needed. Bowtie 1, Bowtie2, and SHRiMP2 have been reported to be fine.

[Nicolas Rosewick]

thanks. I didn't see the other post, sorry ;)