I am not very familiar with bioinfo things as my background is more towards wetlab.
I am analysing my dual RNA-seq results (host+pathogen RNA), and I am using HISAT2 (aligned to genome) + featurecounts pipeline.
I am not sure why I only get assigned reads from unstrand option, when my cDNA libaries are supposed to be built from (KAPA Stranded mRNA-Seq Kit + xGen® Dual Index UMI Adapters), which should be reverse stranded according to instructions online?
Any help will be appreciated.
Yours Sincerely, James PhD student