FeatureCounts troubleshooting

usegalaxy.org support
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The build-in genome option is not responding. Until yesterday evening it would display the options but now it is completely frozen.

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Hi @Sanjukta_Ghosh

I see the indexes now. Please try again and let us know if you also see it.

Also, remember that only a few model mammalian indexes are supported natively.

Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts

Those come directly from the original tool authors.

Other tips:

  1. Make sure that your input BAMs have the database metadata attribute assigned. This is how the “match” between your data and the index is made.
  2. If using some other genome, you can supply the annotation from the history.

One of these FAQs can help with item 2, any tool:

Hope that helps!

3

It is still the same for me. No build-in genome is showing.

Can you elaborate this one: Make sure that your input BAMs have the database metadata attribute assigned. This is how the “match” between your data and the index is made?

I have renamed the collection file. As my Alignment file collection is now renamed, the tool is stuck?

4

Hi @Sanjukta_Ghosh

What is the database assigned to the datasets inside that collection?

Each should have the same database that you want to use from the pull-down menu. The full species name is listed along with a short label commonly called a database or dbkey on most tool forms, but this one just lists the database/dbkey itself.

The part in bold here is the same value that will show up inside the datasets (files) as the database metadata. That’s the technical “match” between the files and the form parameters.

Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts

More help…

Where to find the database metadata

  1. Click into the collection
  2. Expand a dataset
  3. Check the “database” area – if you see a ? then you don’t have one assigned

How to change/add a database to a collection of files

  1. Click on the pencil icon for the collection
  2. On the Edit Attributes pages, on the first tab Database/Build, make a selection then save.

Please give that a try. If you want to share some screenshots we can help more. I’m testing at UseGalaxy.org since that is how you labeled your question.

  • If you are working somewhere else, that will matter for this one, so please share the exact server URL (capture from your browser’s URL bar – just the first part is enough).
  • The tool version might also matter. I’m testing the most current available at UseGalaxy.org. Find the tool name/version at the very top of the form…

featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files (Galaxy Version 2.0.3+galaxy2)

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5

Sorry for replying a bit late. Resolved!

I refreshed the page.

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