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 <j...@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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