[galaxy-user] Removal of duplicates and Cufflinks usage

2011-11-04 Thread Lizex Husselmann
Hi All I've started analyzing my RNA-Seq data for two time points: Day0 and Day4 for control and treated. I've done aligning the data to the reference genome using Tophat. I've removed duplicates from the data sets. Could somebody please tell me, how important is it to remove duplicates and

[galaxy-user] BWA install problem

2011-11-04 Thread Christopher Callaway
Hi, I am trying to run Galaxy locally and downloaded BWA but I can't get it to run. Do I have to use 0.5.6 or can I use 0.5.9? The make command does not work with ver. 0.5.9. Thanks, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way #

Re: [galaxy-user] BWA install problem

2011-11-04 Thread Jennifer Jackson
Hello Christopher, The most current version of the BWA wrapper is designed to work with version 0.5.9. This is true if you are pulling from the development repository or the distribution: http://bitbucket.org/galaxy/galaxy-central/src/21138a4a1fea/tools/sr_mapping/bwa_wrapper.py

[galaxy-user] Uploading Genome from Ensembl

2011-11-04 Thread Scroggins, Sheena
How do I upload the Zebrafish genome from Ensembl to my user history in Galaxy? I'm trying to map my RNA-Seq data using TopHat and need to map it to the Ensembl version of ZFv9, but Galaxy only has the UCSC version built in. The Ensembl version is slightly different. Thanks, Sheena