Thread: cuffmerge error
View Single Post
Old 06-06-2013, 08:51 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

So the chromosome names in your genes.gtf are not matching what you had in the original reference file (your alignments inherited those names).

Compare these two commands:
Code:
awk -F "\t" '{print $1}' genes.gtf | uniq
and

Code:
cat genome.fa | grep ">"

If that is true then you could rename the "Mito" from the genes.gtf to "MT" and then try a re-run.

Last edited by GenoMax; 06-06-2013 at 08:53 AM.
GenoMax is offline   Reply With Quote