hisat2 low overall aligment rate

sunzf · May 27, 2021, 10:39am

i want to align RNA-seq data(mus musculus) to mm10 reference genome,but the alignment outcome just like the image. it seems like i did not alignment with wrong reference genome, but why i get low overall alignment rate? please help me!

sunzf · May 27, 2021, 10:45am

dataset downloaded from GEO: GSE161945

David · May 27, 2021, 3:25pm

Welcome!
Which Galaxy server are you using?