[galaxy-user] min alignement count

Dear Galaxy team, I am performing a differential expression analysis with a cufflinks-cuffmerge-cuffdiff workflow. I was wondering if the default value of 10 fragments for min alignment count is intended to exclude from the significance test all the loci under 10 counts across all samples or

[galaxy-user] Prolonged - Job waiting to run

Dear Galaxy team,   I am running short read alignments with Bowtie for illumina using some data generated from split data using barcode splitter. The alignment programme has been indicated the job waiting to run status for nearly over an hour. I can meanwhile perform other functions such as

[galaxy-user] problem with GenomeSpace Exporter

Dear all, I'm trying to send some data from Galaxy to GenomeSpace, so I can work with this data in Cistrome but I always got this error: GURU MEDITATION: #57662f6109d0460791fa7122116f80ce Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be

Re: [galaxy-user] min alignement count

Hi Davide, I think it it is the first - making it so that both samples in any test would be over this minimum threshold. Best, Jen Galaxy team On 4/12/13 4:28 AM, Davide Degli Esposti wrote: Dear Galaxy team, I am performing a differential expression analysis with a

Re: [galaxy-user] Tool for changes in bedgraph files

Hello Kristen, The tool group BEDTools has two tools that compare bedGraph file directly: Merge BedGraph files and Intersect multiple sorted BED files. This will get you common and unique intervals. If you want to do a finer tuned analysis, a bedGraph file that has the leading