Questions tagged [strandedness]

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R package equivalent to RSeQC infer_experiment to get strandedness of RNA-Seq

I am currently writing an R package that includes a module to run featureCounts (gene quantification tool) from Rsubread. I wanted to be able to specify the correct strandedness option to ...
7
votes
0answers
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Run cuffcompare in strand-agnostic mode

Is there a way to run Cufflinks' cuffcompare in a strand-agnostic mode? I would like to do this because I have some RNA-seq datasets derived from an unstranded run, that should be compared to a ...
1
vote
4answers
217 views

At what processing step should library strandedness type be taken into account?

Suppose I have single-end RNA-seq data for which the reads in the fastq file are reversed with respect to the original extracted RNAs. Suppose I have the following workflow: Map the reads on the ...