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Question: Galaxy HTSeq tool give zero counts
1
gravatar for sch28
9 months ago by
sch28 • 10
sch28 • 10 wrote:

Hi,

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?
rna-seq gtf galaxy counts htseq-count • 602 views
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modified 9 months ago by skhan • 40 • written 9 months ago by sch28 • 10
1
gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: https://galaxyproject.org/support/#troubleshooting

Related prior Q&A (others are in the far right, or can be searched by keyword): https://biostar.usegalaxy.org/p/24210/

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for skhan
9 months ago by
skhan • 40
skhan • 40 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 COMMENT • link written 9 months ago by skhan • 40
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