Re: [galaxy-user] cuff... errors

There was a temporary cluster issue, but it looks like jobs are running again. Try resubmitting your jobs now, and they should succeed. -Dannon On May 1, 2012, at 8:30 PM, Jeremy Coate wrote: > Hi all, > FYI, I've gotten the same error recently when trying to run Bowtie (using > Galaxy Main).

Re: [galaxy-user] cuff... errors

Hi all, FYI, I've gotten the same error recently when trying to run Bowtie (using Galaxy Main). Jeremy On Tue, May 1, 2012 at 4:37 PM, Richard Mark White wrote: > Hi, > Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job > output not returned by PBS: the output datasets wer

[galaxy-user] cuff... errors

Hi, Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. is there a system issue or something with my data? r ___

Re: [galaxy-user] Question about Samtools filter in Galaxy

Hi Kanwar, A simple way is to just treat the SAM dataset as a text file and perform some counts similar to those in this tutorial: https://main.g2.bx.psu.edu/u/aun1/p/galaxy101 The basic outline would be to: 1 - remove unmapped with Filter SAM, "The read is unmapped", "no" 2 - convert sam -> i

Re: [galaxy-user] Mappability

Hi Stuart, If you are able to rsync the Mapability bigWig file from the UCSC downloads server and covert to BED using their compiled tools (also available on same server), then the rest should be fairly straightforward. 1 - Load the data into Galaxy using FTP: http://wiki.g2.bx.psu.edu/FTPUpl

[galaxy-user] Mappability

I want to make an intersection between a few hundreds of genomic intervals (predicted translocation sites from SVDetect) and low mappability regions in genomes (we are working with mm9 right now). UCSC has an excellent mappability track that exactly matches our sequencing data (50 bp kmers), b

[galaxy-user] May 2012 Galaxy Update

Hello all, The May 2012 Galaxy Update is now available ( http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05). *Galaxy Update * is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy U