Question: Galaxy HTSeq tool give zero counts
gravatar for sch28
9 months ago by
sch2810 wrote:


I tried galaxy HTseq tool on BAM file generated by HISAT2 to generated counts. I provided GTF file for both HISAT2 and HTSeq. But HTSeq gave me zero counts for all the genes. Iam not sure how to resolve this issue. Can someone help?

ADD COMMENTlink modified 9 months ago by skhan40 • written 9 months ago by sch2810
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Double check your inputs. Specifically for this problem, start by checking that the GTF file contains gene_id and transcript_id attributes (ideally, these would be distinct values) and that the genome build the GTF is based on is not a mismatch for the genome build mapped against with HISAT2 (check the chromosome identifiers).

FAQs that explain how to do the above:

Related prior Q&A (others are in the far right, or can be searched by keyword):

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson25k
gravatar for skhan
9 months ago by
skhan40 wrote:

I had this same problem. For me it turned out the chromosomes naming was different between the built-in rat genome I was using (e.g. "chr1"), and the GTF I had uploaded (e.g. "1").

ADD COMMENTlink written 9 months ago by skhan40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour