HiSAT2 edit distance option

Question

[gokberk]

Hi all,

I'm analyzing single-end RNA-seq data and was wondering if there is a way to set the edit distance while using HiSAT2. It is not mentioned in the manual, should I somehow arrange the --score-min function?

I was also wondering if there is an option like TopHat's --microexon-search to look for reads that map to microexons.

Cheers, Gökberk

Answer 1

[ynau_kanghuadu]

Hi !

Did you set the 'edit distance' option ? I can't set this option, So, if you can help me, I will very happy.

Thank you. kanghua