Hi Mete,
I am not sure it is the sort problem. I find cufflinks in galaxy is
unstable. I have bam files from Tophat which I can run cufflinks a few days
agao.
But these days when I run cufflinks with these bam files, the error shows.
Strangely, it can work some time. I don't know the reason.
Hi,
Tophat may still be an option for you. You can filter out spliced reads by
filtering column 6 (the CIGAR column) for reads that only map directly (i.e.
c6=='56M' if you have a 56bp paired end read). But I agree with Jen that most
likely it is a sort problem.
Best Wishes,
David.
Hi,
The main Galaxy server is failing to schedule tophat's jobs. Giving error:
Unable to queue job for execution. Resubmitting the job may succeed.
I've been able to run other tools jobs.
Thanks,
Carlos
___
The Galaxy User list should be
This problem went away. Thanks.
On Tue, Aug 9, 2011 at 10:55 AM, Carlos Borroto
carlos.borr...@gmail.com wrote:
Hi,
The main Galaxy server is failing to schedule tophat's jobs. Giving error:
Unable to queue job for execution. Resubmitting the job may succeed.
I've been able to run other
Hi jen, have 4 biological samples, the RNA-seq data for each sample
have 8 to 9 fasq.gz files with each file about 350 MB.
So this is within the limit by public galaxy.
Tao
-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Tuesday, August 09, 2011 4:03 PM
To:
Hi,
I think you need to include a track line and specify bedgraph, like this
track type=bedGraph
Is that maybe the problem? It sounds like UCSC is treating your file
as a standard bed, which it will do without the track line.
Jim
On Tue, Aug 9, 2011 at 11:32 PM, John Wu
Hi Jim:
Thanks for your help!
I know how to make a bedgraph file, but it's just that I thought galaxy
could automatically make a bedgraph file ( or track ) out from a text file.
Maybe I was thinking wrong.
John
-Original Message-
From: James Robinson
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