Problems with GTF file

[jennaj]

Hello,

You’ll need to unpack the iGenome archive and just upload the GTF dataset:

@jennaj

For iGenomes , the archive corresponding to the target genome/build needs to be locally downloaded, the tar archive unpacked, and then just the genes.gtf data uploaded to Galaxy (browse the local file, or use FTP). Find all available genome/builds here: iGenomes

@Joe_Hoolachan

I uploaded this tar.gz as GTF on galaxy and encountered no issue with that part. In addition, when used as a GTF for featurecounts from my HISAT2 reads directly there was no issue.

I would suggest reviewing those results. Suspect the GTF was not actually used correctly.

FAQ: Loading Data

Thanks!