Mapping stranded smallRNA reads with TopHat

[JonB]

Hi,

I have short reads (max 50 nts, mostly 20-40 nts) that are from a stranded ligated Illumina library. I could't find if Bowtie2 has a stranded option so I use the TopHat fr-secondstrand option. But I don't expect my reads to be spliced so is there an option to skip the read segmentation? Or should I use other mappers for this job?

Thanks,

Jon

[GenoMax]

You can try the subread aligner and featureCounts downstream.