htseq-count
Stranded libraries
If you have a stranded library you have to set the Stranded parameter of htseq count in Galaxy. Remarkably the default setting of this parameter is Yes. However, in reality for all recent stranded libraries the setting of this parameter should be Reverse. (For unstranded libraries you obviously select No.)
- very clear explanation of strandedness and how to check it
- topic on RNASeq libraries in the NGS introduction course: explanation on how to generate a stranded library
Quizzes