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
************************************************
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
