Question: Galaxy HTSeq tool give zero counts
gravatar for sch28
17 days ago by
sch280 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 13 days ago by skhan30 • written 17 days ago by sch280
gravatar for Jennifer Hillman Jackson
14 days ago by
United States
Jennifer Hillman Jackson24k 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 14 days ago • written 14 days ago by Jennifer Hillman Jackson24k
gravatar for skhan
13 days ago by
skhan30 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 13 days ago by skhan30
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