Help in testing alligning this one RNA-seq data

Question

[qmarulfiz]

Hi,

I am new and learning RNA-seq bioinformatic analysis on my own. Can someone try alligned one of the run in GSE147846 study dataset. I try to HISAT2 using useGalaxy and everytime I did I get overal allingment less thant 2%. This cannot be right.

Just want to know whether I am doing it right or wrong only.

Thank you in advance!

[Arup Ghosh]

The GEO accession contains datasets generated using Bisulfite-Seq and you have to use a different alignment tool like HISAT-3N or Bismark.

[qmarulfiz]

Thank you!, I just figured it out last week. Going to try again later. Thanks for the suggestion