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Old 10-29-2015, 10:25 AM   #1
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Location: Rockville, MD

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Default strand-specificity in RSEM


I'm trying to figure out the settings for analysing strand-specific RNA-Seq data from Illumina TruSeq chemistry with rsem-calculate-expression

Specifically, regarding the "--forward-prob" parameter, the manual has this to say:

"....Set to 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. (Default: 0.5)"

Question: based upon my understanding of the molecular biology of the TruSeq strand-specific kit, the strand actually getting sequenced in read 1 of a pair is the cDNA sequence, (or in RSEM manual terminology, the reverse strand).

As such, my hunch is that I should be using --forward-prob=0, but I'd like to check with the community to see if I'm getting things right here.

Any help much appreciated,


shurjo is offline   Reply With Quote

rna-seq, rsem, stranded, truseq

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