Hi,

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
[stephen@biosc-sub2-169]$

I chaged the input variables and it returned 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 and maybe in a different format to the cufflinks output.

The Tophat index that was used to map the reads H. sapiens, UCSC hg19 downloaded from http://bowtie-bio.sourceforge.net/index.shtml

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!