Question: Locally cached annotation not available for featureCounts
0
gravatar for 116224719
7 months ago by
1162247190
1162247190 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 galaxy • 189 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson24k • written 7 months ago by 1162247190
0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson24k 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 7 months ago • written 7 months ago by Jennifer Hillman Jackson24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 103 users visited in the last hour