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4 months ago
pubsurfted ▴ 40
I'm having trouble trying to figure out how to determine the directionality of paired-end reads. I want to find whether the reads are unstranded, first stranded or second stranded. The tool suggestions I've got so far are : Salmon, RSeqC, and how_are_we_stranded_here. Does anyone have anyone experience using these? Which one do you recommend.
Easiest is to run infer_experiment.py after mapping your reads against the reference genome.
Not everyone maps rna-seq reads to reference genome to get bam files (I rarely do this because you can't plug bam genome alignments into probabilistic rna-seq models which are required for accurate rna-seq quantification).
The question here is not whether everyone maps the reads against the genome or not. But if you want to use infer_experiment to infer the strand, this is a requirement.
The existing tools you listed are fine; any one of them works.