I am trying to analyse my mRNAseq data using the galaxy reference based workflow (Reference-based RNA-Seq data analysis). I am very new to data analysis and also to galaxy. I tried two different approaches to align my data:
1)RNA-STAR followed by feature counts: In this case the feature counts showed 0 counts.
2) Next, I tried HISAT2 alignment…and that showed just 177 reads…
I don’t understand why the read number is so low…do you have any suggestions?