[galaxy-user] May 2012 Galaxy Update

2012-05-01 Thread Dave Clements
Hello all, The May 2012 Galaxy Update http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05is now available ( http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05). *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates * is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy

[galaxy-user] Mappability

2012-05-01 Thread Brown, Stuart
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),

Re: [galaxy-user] Mappability

2012-05-01 Thread Jennifer Jackson
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:

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

2012-05-01 Thread Dannon Baker
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).