Does StringTie need strand information if HISAT2 was run with strand-specific information

Question

[piyushjo]

Hi,

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?

Thanks!

[humeira.tayyab]

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

[piyushjo]

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