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Question: Content of the built-in hg38 genome annotation available in Featurecounts
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gravatar for mercedes.bentata
6 months ago by
mercedes.bentata • 30
mercedes.bentata • 30 wrote:

Hello, After executing featureCounts on my BAM file using a built-in genome (hg38) from Galaxy I have obtained the table with the Geneids and the number of reads mapped to them. I am trying to find where is the built in annotation file in Galaxy in order to know to which gene/feature each of the Geneids (numbers) reffer to. But I don't manage to find it. Does someone know where can I find the annotation file? Thank you, Mercedes
built-in annotation featurecounts galaxy rna-seq • 387 views
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modified 6 months ago by mblue9 • 140 • written 6 months ago by mercedes.bentata • 30
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gravatar for mblue9
6 months ago by
mblue9 • 140
mblue9 • 140 wrote:

Hi Mercedes,

The built-in annotation files used by featureCounts can be found within the Subread package here: https://sourceforge.net/projects/subread/files/

But those files have no gene names, just the Entrez gene identifiers (e.g. 497097). If you want gene names you can get those for the Entrez identifiers with the annotateMyIDs tool in e.g. this Galaxy https://usegalaxy.eu/.

Hope that helps!

P.S. I've added some info on the annotation to the featureCounts wrapper now.
ADD COMMENT • link written 6 months ago by mblue9 • 140

Thank you very much for the answer. Is there a similar tool like annotateMyIDs but in the main Galaxy (https://usegalaxy.org/) in order to get the gene names?

ADD REPLY • link written 5 months ago by mercedes.bentata • 30

Hi - This tool is not installed at https://usegalaxy.org. I made a request to have it added. Please follow progress here: https://github.com/galaxyproject/usegalaxy-playbook/issues/141

The tool UniProt ID mapping and retrieval can convert many identifiers, but not Entrez gene IDs.

Workaround: If most of your work is at https://usegalaxy.org, you could just transfer the file you want to convert IDs on over to https://usegalaxy.eu, use the tool, then send the results back. To transfer individual datasets, control-click the disc icon to copy the dataset URL and paste it into the Upload tool.

Jen, Galaxy team

ADD REPLY • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k
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