Locally cached annotation not available for featureCounts

Question: Locally cached annotation not available for featureCounts

16 months ago by

116224719 • 10 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 • 640 views

ADD COMMENT • link •

modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by 116224719 • 10

6 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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/

Preparing and using a Custom Reference Genome or Build https://galaxyproject.org/learn/custom-genomes/#custom-builds
How do I find, adjust, and/or correct metadata? https://galaxyproject.org/support/metadata/

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

16 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »