small RNA annotation using --locifile file

MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes

MIT License

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small RNA annotation using --locifile file #96

Closed atvivek closed 3 years ago

atvivek commented 4 years ago

I have used Shortstack for some time now but I don't understand how to include strand information other than Chr:start-end in the loci file to annotate accordingly. Any help on this would be greatly appreciated.

Regards, A.T.Vivek

BioFalcon commented 4 years ago

Might want to look at the --strand_cutoff parameter. If your reads align to both strands and do not pass the threshold, ShortStack will not assign a strand.

atvivek commented 4 years ago

Thanks@BioFalcon. Your suggestion was helpful.