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Old 01-10-2013, 06:05 AM   #1
Location: Cork

Join Date: Nov 2012
Posts: 13
Default Cuffmerge Issue


Can somebody please help/advise with this cuffmerge issue?

I am having an issue with merging the cufflinks transcripts.gtf file with cuffmerge. I have two files that I need to merge, the command is as follows

cuffmerge -g genes.gtf -s /mnt/yabba/yoda_backup/var/data/hg19.fa assemblies.txt

The output file merged_asm is completely empty! I have run this now a number of times and still no output.

I am not receiving any errors and simulation finishes after 5 secs, as per below.

[Thu Jan 10 13:00:48 2013] Beginning transcriptome assembly merge

[Thu Jan 10 13:00:48 2013] Preparing output location ./merged_asm/
[Thu Jan 10 13:00:53 2013] Converting GTF files to SAM

I chaged the input variables and it kept returning errors. However, I created a blank .txt doc called genes.gtf and ran the command, this produced the same result as above, no errors and no output.

I believe the genes.gtf file is not being read correctly any maybe in a different format to the cufflinks out put.

The Tophat index that was used to map the reads H. sapiens, UCSC hg19 downloaded from

The genes.gtf file being used came from ftp://igenome:G3nom3s4u@ussd-ftp.ill...SC_hg19.tar.gz

They are both from UCSC hg19 so I wasn't expecting any compatability issue.

Can somebody please advise?

Many thanks in advance!
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