RNAseq (TruSeq stranded total RNA) - Stringtie fr-firststrand??
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!
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Stranded Tru-Seq protocol is fr-firststrand in Stringtie/Cufflinks/Tophat and related Tuxedo software. https://chipster.csc.fi/manual/library-type-summary.html
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