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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Question to StrigTie and the use of strand-specific data #323

Open cc-prolix opened 3 years ago

cc-prolix commented 3 years ago

Hello! I have a question regarding the use of StringTie for assembly and merging of assembled annotations: I am working on a RNA-seq pipeline: I use HISAT2 for strand-specific alignment and its BAM files as input for stringtie further down the line...When I use StringTie for assembly, do I have to specify the --rf/--fr options or is the information from HISAT2 sufficient? What would be best practice? Further, I have seen people use the --rf/--fr options when using stringtie --merge mode. I wouldn`t have thought to specify strand info here so I wanted to ask again what would best practice be?

Thank you very much for your help!