RNAseq (TruSeq stranded total RNA) - Stringtie fr-firststrand??

Question

[JirMan]

If I have RNAseq data from an Illumina TruSeq Stranded protocol, do I have to include the --rf (assumes a stranded library fr-firststrand) or the --fr (assumes a stranded library fr-secondstrand) in the Stringtie analysis?

Thank you in advance!

Answer 1

[grant.hovhannisyan]

Stranded Tru-Seq protocol is fr-firststrand in Stringtie/Cufflinks/Tophat and related Tuxedo software. https://chipster.csc.fi/manual/library-type-summary.html

[JirMan]

Thank you very much for your reply and the link, it's very helpful :)

[grant.hovhannisyan]

glad to help! please accept the answer to close the thread.