Question: Locally cached annotation not available for featureCounts
1
gravatar for 116224719
10 months ago by
11622471910
11622471910 wrote:

Hi all,

For my RNAseq analysis, I am using the featureCounts tool to measure gene expression from SAM or BAM files. I want to use a locally cached annotation of the human genome but there are no annotation available. Who should I contact? Galaxy says to contact Galaxy Administrator, but I can't find any info about how to contact them...

Thanks for the help,

rna-seq featurecounts galaxy • 315 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson25k • written 10 months ago by 11622471910
1
gravatar for Jennifer Hillman Jackson
5 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Update

Things change! The latest featurecounts wrapper now has a built-in annotation for a few model organisms. See the tool form for those currently included.

When using the built-in annotation, the database metadata attribute must be assigned to the BAM dataset.

When using annotation from the history, the database must be assigned to both the BAM and GTF datasets, and be a match.

If you are using a Custom Genome, then it should be promoted to a Custom build first, then assign the new custom database to both the BAM and GTF inputs.

FAQs: https://galaxyproject.org/support/

ADD COMMENTlink modified 5 days ago • written 5 days ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There is no natively cached reference annotation for this tool at Galaxy Main (http://usegalaxy.org) and most likely never will be.

Instead, upload sourced annotation data that is a match for your genome/build as a dataset and use it "From the history".

It is very important that the genome build is exactly the same between all inputs (for this and all other tools). How to avoid a reference genome mismatch problem is covered in this FAQ: https://galaxyproject.org/support/chrom-identifiers/

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson25k
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