[galaxy-user] (no subject)

Hi, I uploaded some file that resulted to be too big and my history showed that that was not more space available. Now I deleted few file, and I should have 80 GB available, but my history shows still that I have no more space available for analysis. Can anyone from the Galaxy team check this f

[galaxy-user] problem with cuffdiff

Hy guys, I am performing some RNA sequencing. I am using a gtf file as a reference annotation for the cufflink - cuffmerge steps. Then when I do the cuffdiff I find something strange. Where there is the gene name, the corresponding values (all of them!) are 0, where there is no gene name there a

[galaxy-user] (no subject)

Hi, I have worked so far on the free web-based version of Galaxy; now I have installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot access to my data (stored on the web version of Galaxy) using Galaxy on Bio Linux. If it is possible, does anyone know how to do it? Thanks,

[galaxy-user] problem with the public Main Galaxy server

Hi, is anybody else experiencing problems with the public Main Galaxy server at http://main.g2.bx.psu.edu? It just does not work anymore. Any suggestion? Giuseppe Ianiri ___ The Galaxy User list should be used for the discussion of Galaxy a

[galaxy-user] cufflink workflow

Hi, I want to compare gene deferentially expressed in two conditions (1 and 2). I don't have a GTF reference annotation. In my first attempt, I mapped my Illumina reads with TopHat. Then I run Cufflink, and Cuffmerge on my Cufflink outputs for the conditions 1 and 2. At the end, I run Cuffdiff u

[galaxy-user] software post alignment

Hello, I performed my mapping using tophat - cufflink - cuffmerge - cuffdiff. With the information I have for my analysis so far, I can reannotate wrong genes, check for correct splicing etc. However, I would like to perform some analysis post-alignment, like for example samples clustering, volcano

[galaxy-user] compare two dataset

Hi all, I got my cuffdiff output and I have to compare results from two (or eventually more) different dataset. Does anybody know if there is a way to do that on Galaxy? Also more in general, is there a manual for the Galaxy tools? That would be very helpful for someone who is new on the field (l

[galaxy-user] Cuffdiff without gene annotation

Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff output gene and transcript differential expression testing I filtered some data. For example, for two samples I got about 400 gene and 900 transcript differential expressed with fold change >2. Since I a

Re: [galaxy-user] filter for +/- 2-fold difference in expression levels

From: Jennifer Jackson [j...@bx.psu.edu] Sent: Thursday, November 29, 2012 10:51 AM To: Ianiri, Giuseppe Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] filter for +/- 2-fold difference in expression levels Hello Giuseppe, Fold is included in the Cuffdiff output. Section

[galaxy-user] filter for +/- 2-fold difference in expression levels

Hey guys, I have my Cuffdiff output and I was trying to figure out how to get the data I need. I am interested in the outputs Transcript and Gene differential expressed. Does anyone know how to filter for +/- 2-fold difference in expression levels? Thank you Giuseppe Ianiri, Ph.D. Division of C