Tools for strand direction detection RNA-Seq

Question

[pubsurfted]

Hello everyone.

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.

[iraun]

Easiest is to run infer_experiment.py after mapping your reads against the reference genome.

[dsull]

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).

[iraun]

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.

[dsull]

The existing tools you listed are fine; any one of them works.