Strand-specific in HT-Seq
Hello everyone,
I'm going through some published RNA-seq data and I'm about to start quantifying the abundance of transcripts with HT-Seq, however I don't know what to put in strand-specific (-s <yes/no/reverse>) . In the article description it indicates that TruSeq Stranded Total RNA was used, can you help me?
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There are multiple threads about this issue on biostars but here is a tool that can be used without alignments: GUESSmyLT guess the library type of your RNA-seq data (orientation, strandness)
More info: Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
thanks so much, I will try this tool.
Depends on the library preparation, if your cDNA is reverse complement then it should be -s <reverse>.