Hi! I am getting this error when I try to run stringtie on some RNA-seq data. This is what I am getting.
WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences.
I am using a gtf file from flybase. I am wondering if it is just not the correct file? I am working on a project with Drosophila. Does anyone know anything about this or could help?
The index that I used for hisat2 was just the premade Drosophilia index they have on their site. Could it be an issue of the index is a older version than the gtf file?
Thanks in advance