Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: featureCounts doesn't recognize Rat annotation file in history, what am I doing wrong?
0
gravatar for andrewzlobin
5 months ago by
andrewzlobin • 20
andrewzlobin • 20 wrote:

Dear Experts, I use Htsat2 output file for running feature-counts, but when I set up the run Galaxy doesn't t recognize Rat annotation file in history(Rattus_norvegicus.Rnor_6.0.92.gtf, which I uploaded) what am I doing wrong?
rna-seq tool gtf datatype metadata • 198 views
ADD COMMENT • link •
modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by andrewzlobin • 20
0
gravatar for Jennifer Hillman Jackson
5 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

First, the tool form option Gene annotation file should be set to "in your history". GTF datasets will appear in the select menu.

The database metadata assignment should be the same between all inputs. Also, the datatype metadata assignments must be made to all. It is very important that the genome build/version is the same for all inputs/steps (have content with respect to the same "database") or tool errors will result.

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

  • My job ended with an error. What can I do?
  • Common datatypes explained
  • The tool I'm using does not recognize any input datasets. Why? << Try this first
  • How do I find, adjust, and/or correct metadata?
  • Mismatched Chromosome identifiers (and how to avoid them) << Make sure the genome mapped against is a match for your annotation, or find another source that is. iGenomes is one choice for rn6 UCSC based annotation: https://support.illumina.com/sequencing/sequencing_software/igenome.html. Download the tar archive locally, uncompress it, and upload just the genes.gtf file to Galaxy.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 168 users visited in the last hour