Strand-specific in HT-Seq

Question

[sansan96]

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?

[GenoMax]

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

[sansan96]

thanks so much, I will try this tool.

[PK]

Depends on the library preparation, if your cDNA is reverse complement then it should be -s <reverse>.