Question: Does StringTie need strand information if HISAT2 was run with strand-specific information
gravatar for piyushjo
8 months ago by
piyushjo290 wrote:


I performed my alignment using HISAT2 with strand-specific infromation: --rna-strandness RF. And then I used StringTie to quantify BAMS without --rf tag, now I am concerned if StringTie assumed the libraries to be unstranded. I tried finding some answers on other sources (github), where gpertea (@Github) sort of mentioned that HISAT2 takes care of it; but I didn't find a straight answer.

Also I have other reads aligned with STAR where I didn't use any --rf/--fr information for downstream analysis with StringTie, but the libraries had strand-specific information. Do you suggest I re-run StringTie with appropriate tag for STAR aligned sequences?

Could you help me with it?


hisat2 stringtie • 327 views
ADD COMMENTlink modified 6 weeks ago by humeira.tayyab10 • written 8 months ago by piyushjo290

Did you find the answer to this problem? I am also confused about using rnastrandness option in stringtie after using it in Hisat2.

ADD REPLYlink written 6 weeks ago by humeira.tayyab10

Yup. If you specify --rna-strandness in the hisat2 run itself, then you don't need to to mention that with stringtie. Look at the "Alignment" and "Expression" section of this tuorial. They specified strandness in hisat2 but not in stringtie. Good luck!

ADD REPLYlink written 6 weeks ago by piyushjo290
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1199 users visited in the last hour