Question: DESeq2 couldnt run due conflict in annotation
gravatar for Wanderer
15 days ago by
Wanderer10 wrote:

Hi, I was trying to run DESeq2 but some error is happening:

Error in summarizeToGene(txi, tx2gene, ignoreTxVersion, countsFromAbundance) :

None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that you are using the same annotation for both.

Would anyone know what transcripts annotation the DESeq2 from galaxy uses in the gene name?? I was trying with refGene and UCSC and both could'nt run.


ADD COMMENTlink modified 15 days ago by Jennifer Hillman Jackson24k • written 15 days ago by Wanderer10
gravatar for Jennifer Hillman Jackson
15 days ago by
United States
Jennifer Hillman Jackson24k wrote:


This type of error usually indicates a genome mismatch problem between the reference GTF used with DeSeq2 and the reference genome (or transcriptome) used for upstream mapping.

Support FAQ troubleshooting help:

All FAQs:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 15 days ago by Jennifer Hillman Jackson24k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 108 users visited in the last hour