reverse strandedness -ss 1 or -ss 2 about sprint

[jumphone]

Hi, please check the manual of SPRINT ( typically, -ss should be 0 ):

-­‐ss INT

when input is strand-­‐specific sequencing data, please clarify the direction of read1. [0 for antisense; 1 for sense] (default is 0)

[ojziff]

Thanks @jumphone for quick response.

Input is reverse stranded RNAseq made with TruSeq Stranded mRNA kit. Reading https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-mrna.html I think it is antisense rather than sense. Please could you confirm should -ss be 0 for TruSeq Stranded mRNA?

[jumphone]

Hi,

I saw a sentence in the manual of TruSeq Stranded mRNA kit: "Strand specificity is achieved by replacing dTTP with dUTP in the SMM (Second Strand Marking Mix), followed by second strand cDNA synthesis using DNA Polymerase I and RNase H."

In my experience, for data using "dUTP" step, "-ss" should be "0".

Thanks for using SPRINT.

[ojziff]

Very helpful, thank you!