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 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 http://bowtie-bio.sourceforge.net/index.shtml
The genes.gtf file being used came from ftp://igenome:[email protected]_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!
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 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 http://bowtie-bio.sourceforge.net/index.shtml
The genes.gtf file being used came from ftp://igenome:[email protected]_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!