Question: DESeq2 couldnt run due conflict in annotation
0
gravatar for Wanderer
7 months ago by
Wanderer10
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.

Thanks!

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by Wanderer10
0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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: https://galaxyproject.org/support/chrom-identifiers/

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

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
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