featureCounts jobs will not submit unless input BAM(s) have the "database" metadata assigned

Question: featureCounts jobs will not submit unless input BAM(s) have the "database" metadata assigned

6 months ago by

Hello, I am trying to run featureCounts on my BAM file using a built-in genome from Galaxy. I wrote "hg38" in the "Select built-in genome" option and when I try to excute this message appears me: "Parameter bgenome requires a value, but has no legal values defined." Maybe, the built-in genome name (hg38) I wrote is not correct. Do you know what is the correct file name? or where can I find the names of the files? Thank you very much, Mercedes

featurecounts metadata database rnastar bam • 306 views

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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by mercedes.bentata • 30

6 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool requires that the input BAM has the database assignment made. RNA STAR should be doing this at runtime, but it isn't, and that may be a bug (we are doing some testing).

Solution for now: Manually assign the database "hg38" to the input RNA STAR bam dataset and this error will go away. There are several patch versions, so be sure to assign the primary release: Human Dec 2013 (GRCh38/hg38) (hg38)

How do I find, adjust, and/or correct metadata? https://galaxyproject.org/support/metadata/

Thanks for reporting the issue!

Jen, Galaxy team

ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

Update

For anyone having trouble with the Featurecounts tool recognizing BAM/GFT inputs, please know that the tool now requires that the database metadata assignment is made to both the BAM and GTF inputs (when sourced from the history).

Please see this post for full details: https://biostar.usegalaxy.org/p/24154/#28027

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

Hello, Thank you very much for your answer! Now it's working. 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. Thank you, Mercedes

ADD REPLY • link written 6 months ago by mercedes.bentata • 30

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