I have aligned my data by using Hisat2, now in next step i just want to use HtSeq for counting reads, but getting following error.
please suggest an solution for this issue
please suggest an solution for this issue
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Hi @Ashish_DR
The setting are specifying to count up by the gene_id and exon features, but those are not present in your reference annotation. This results in an error.
You can either adjust the settings to match the attributes in your current annotation or use a different annotation.
GTF works better than GFF3 for most people, and there is much prior Q&A around that at this forum. I added a few tags to help you find those.
You can also review these FAQs for help addressing this and related problems that often come up together. These problems can present whether you are working in Galaxy or not.
- #working-with-gff-gft-gtf2-gff3-reference-annotation
- #working-with-very-large-fasta-datasets
- #mismatched-chromosome-identifiers-and-how-to-avoid-them
Hope that helps!