# Getting error while using HtSeq Count

**URL:** <https://help.galaxyproject.org/t/getting-error-while-using-htseq-count/9017>\
**Category:** Uncategorized\
**Tags:** troubleshooting, transcriptomics, reference-annotation\
**Created:** [November 14, 2022, 6:26am UTC](https://help.galaxyproject.org/t/getting-error-while-using-htseq-count/9017 "2022-11-14T06:26:29Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [November 17, 2022, 12:19am UTC](https://help.galaxyproject.org/t/getting-error-while-using-htseq-count/9017/2 "2022-11-17T00:19:00Z")

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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](https://training.galaxyproject.org/training-material/faqs/galaxy/#working-with-gff-gft-gtf2-gff3-reference-annotation)
- [#working-with-very-large-fasta-datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/#working-with-very-large-fasta-datasets)
- [#mismatched-chromosome-identifiers-and-how-to-avoid-them](https://training.galaxyproject.org/training-material/faqs/galaxy/#mismatched-chromosome-identifiers-and-how-to-avoid-them)

Hope that helps!

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