# Feature counts built-in annotation file - no options available

**URL:** <https://help.galaxyproject.org/t/feature-counts-built-in-annotation-file-no-options-available/13776>\
**Category:** Uncategorized\
**Tags:** transcriptomics, reference-annotation, tool-help, featurecounts\
**Created:** [October 28, 2024, 12:16am UTC](https://help.galaxyproject.org/t/feature-counts-built-in-annotation-file-no-options-available/13776 "2024-10-28T00:16:08Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Ken\_Saville](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/ken_saville/32/6228_2.png) [@Ken\_Saville](https://help.galaxyproject.org/u/Ken_Saville)\
**Post date:** [October 28, 2024, 12:16am UTC](https://help.galaxyproject.org/t/feature-counts-built-in-annotation-file-no-options-available/13776/1 "2024-10-28T00:16:08Z")

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I’m trying the RNA seq tutorial - reads to counts.

I’ve done the Hisat2 mapping and am trying to do the counting

I selected the feature counts tool

and selected featurecounts built in for the annotation files

But it says no options available

I need the mm10 annotation file

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**Author:** ![Ken\_Saville](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/ken_saville/32/6228_2.png) [@Ken\_Saville](https://help.galaxyproject.org/u/Ken_Saville)\
**Post date:** [October 28, 2024, 12:18am UTC](https://help.galaxyproject.org/t/feature-counts-built-in-annotation-file-no-options-available/13776/2 "2024-10-28T00:18:29Z")

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Here’s a link to my history

> **[Galaxy](https://usegalaxy.org/published/history?id=9efa898e227624e2)**
>
> Galaxy is a community-driven web-based analysis platform for life science research.

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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [October 28, 2024, 8:03am UTC](https://help.galaxyproject.org/t/feature-counts-built-in-annotation-file-no-options-available/13776/3 "2024-10-28T08:03:06Z")

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Hi @Ken_Saville,  
same issue reported just a bit earlier here: [Tool update: featureCounts · Issue #6445 · galaxyproject/tools-iuc · GitHub](https://github.com/galaxyproject/tools-iuc/issues/6445)

While this is getting fixed, you can do what Teresa suggests there:  
Set the `Gene annotation file` to → `featureCounts built-in` first, only then select the input collection.

Sorry for the inconvenience,  
Wolfgang