Hello. I am trying to use HTseq count for my data. I am using the bam file and a gff file of the human reference genome from ncbi. I have been getting this error. Any help on how to go about this?
[bam_sort_core] merging from 64 files and 1 in-memory blocks…
Error occured when processing GFF file (line 17484 of file /scratch/user/galaxy/maroon_galaxy/objects/2/5/9/dataset_259335c3-5a5c-4d34-8eef-876dfc014a1d.dat):
unmatched quote
[Exception type: ValueError, raised in _HTSeq.pyx:1576]
Hi @larad
it is hard to identify the issue without looking into data and the log file.
Have you mapped reads in Galaxy? If yes, have you used “built-in” reference genome in the mapping step? If yes, maybe try featureCounts and change Genome annotation file to featureCounts built-in. Try another annotation file, preferably from GenCode. Make sure you use the annotation file for the same version of genome assembly, as in the mapping step.
Kind regards,
Igor