[galaxy-user] extracting, stitching, converting MAF files: interval_maf_to_merged_fasta.py: command line usage?

Dear Galaxy team / user mailing list, my question is with respect to command line usage, not about interactive / web-based Galaxy usage. Regarding the publication [1], section 2.3 Stitchers. I want to use the stitcher to extract a given region from MAF files, stitch it together and convert it to

[galaxy-user] tophat output spice junction output

Hi, where can I find an explanation of the columns in the splice junctions output? From 7 to12 they are only numbered thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

Re: [galaxy-user] cuffdiff failed

Hello Irene, There appears to be a problem with the information entered into the tool form for the labels (e.g. Group name). The command string only shows one group label value when there are two group data sets. You submitted a bug report for this same issue, so I will take a look there at

[galaxy-user] Problem setting up admin in Galaxy local instance!

Dear all, Please help me figure out what went wrong to set up ADMIN in my local instance using the new retinaMBP! This is what I did 1. I changed universe_wsgi.ini.sample file into universe_wsgi.ini (using Mac TextEdit) 2. Then, I edited universe_wsgi.ini as followed: # Administrative

Re: [galaxy-user] Problem setting up admin in Galaxy local instance!

Hi Di, You need to remove the starting comment/hash from the admin_users line: admin_users = dkngu...@uw.edu Thanks for using Galaxy, Dan On Jul 20, 2012, at 5:13 PM, Di Nguyen wrote: Dear all, Please help me figure out what went wrong to set up ADMIN in my local instance using the

[galaxy-user] flaking regions across TSS

I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites using this post steps https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html Now what I would like to do is to get 5000 bp upstream an downstream using flank tool in galaxy, but i realize

[galaxy-user] Cuffconfusion

ok, im really confused now about cufflinks and its tools. All I wanted was to look for differentially expressed genes between two samples: treated (2 replicates) and control (one replicate). can anyone give me a workflow for a similar analysis with the various options chosen? I have read a lot

Re: [galaxy-user] Cuffconfusion

There is an excellent article on how to do differential gene/transcript expression with Tophat and Cufflinks here: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html This article will answer the questions you've posed below and provides numerous figures that will help you

Re: [galaxy-user] flaking regions across TSS

Hello Kanwar, On 7/20/12 3:31 PM, shamsher jagat wrote: I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites using this post steps https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html Now what I would like to do is to get 5000 bp