What number I should specify for SMARTer Stranded Total RNA-Seq Kit v2 for --forward-prob in RSEM?

Question

[John]

Hi

I have single end RNA seq data with library prepard using SMARTer® Stranded Total RNA-Seq Kit v2. What is the value for --forward-prob in RSEM-estimate-expression?

I know it is 1 for a strand-specific protocol where all (upstream) reads are derived from the forward strand, 0 for a strand-specific protocol where all (upstream) read are derived from the reverse strand, or 0.5 for a non-strand-specific protocol. But I don't know how to identify forward or reverse strand.

Thanks

Answer 1

[tjbencomo]

Based on the schematic on the kit's website and this blog post about different types of kit stranding, it looks like you should use –forward-prob 0 as it is reverse stranded