Topic
Strandedness
Is my library stranded, and did I count reads with the right strand setting?
Guessing the wrong strand setting silently loses half your counts or assigns reads to antisense genes. A single run of RSeQC infer_experiment or salmon's library-type detection resolves it in a minute, before any counting.
- How to Check Library Strandedness in Bulk RNA-seq
One minute with infer_experiment.py or salmon -l A tells you which strand flag to use, before a wrong guess quietly eats your counts.