Hello, Dr. Jeremy Goecks already sent me an response that fixed the problem (perhaps forgetting to email the list as well)- I was using unsorted output directly from Bowtie. When I tried using a TopHat BAM file it worked. Thank you for your reply! -David On Jun 10, 2011 4:58pm, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello David,
Cufflinks requires locally cached data to perform the Bias Correction function.
Without seeing any sample data, a quick guess is that changing the option "Tool: Cufflinks -> Perform Bias Correction:" from yes to no in that workflow step will probably correct the problem.
Another option is to set the dbkey value in the initial input FASTQ file to be a native database (if possible).
Hopefully this helps, but if does not correct the problem, please share a history link with data that demonstrates the problem and I can take closer look (emailing link to me directly, to maintain data privacy, would be fine).
Jen
Galaxy team
On 6/8/11 12:07 PM, David Robinson wrote:
Hello,
When I attempt to run cufflinks based on .sam output from bowtie I get
an error:
An error occurred running this job: /cufflinks v1.0.1
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 8 -b
/galaxy/data/hg19/sam_index/hg19.fa
Error running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf'
/What can I do to get around this problem and run cufflinks?
My workflow is on http://main.g2.bx.psu.edu and can be found here (I ran
it using a .fastq file):
http://main.g2.bx.psu.edu/u/dgrtwo/w/cufflinks-workflow-imported-from-upload...
Thanks in advance for your help!
-David
************************************************
David Robinson
Graduate Student
Lewis-Sigler Institute for Integrative Genomics
Carl Icahn Laboratory
Princeton University
646-620-6630
************************************************
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Jennifer Jackson