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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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stranded libraries #59

Closed damiankao closed 8 years ago

damiankao commented 8 years ago

I am using Hisat2/Stringtie to assemble a set of reference annotations from multiple libraries. I am following the procedure laid out on the Stringtie website.

Some of the libraries were created with stranded prep chemistry. I mapped those libraries with hisat2 using the --rna-strandness FR along with the --dta flag.

Will Stringtie take into account the libraries with strand information during the merge step?

gpertea commented 8 years ago

StringTie does not get (hence does not use) this library-level information directly -- though this information should be reflected in the spliced-alignment strand info of the alignments generated by HISAT2 --dta (the "XS" tag) which of course StringTie uses when it assembles the read alignments into transfrags.