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-uploaded-file
>
>
>
> 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
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