[galaxy-user] problem in saving visualizations in trackster

2011-07-12 Thread suman pal
Hello, I am registered as jiga...@yahoo.com in Galaxy main. recently I am trying to save visualizations in Trackster and repeatedly getting a message unable to save visualization.Is this something related to my PC memory ?This is in reference to RNAseq track visualization while adding tracksGala

Re: [galaxy-user] finding open reading frames and corresponding genes

2011-07-12 Thread Jennifer Jackson
Hello, Making the assumption that your data is DNA (and not RNA), the tools under "NGS: SAM Tools" and "Operate on Genomic Intervals" can generate coordinates of the mapped reads which then can be correlated with known genes/ORFs from your bacterial genome (or related genomes, if you can obta

[galaxy-user] cufflinks output in UCSC browser

2011-07-12 Thread Aleks Schein
Hi all, I am doing cufflinks assembly of TopHat-aligned NGS reads with Refseq gene track as reference annotation. All works, but resulting gtf files cannot be displayed in UCSC browser. I use "display at UCSC main" link, but get a message:"Error 500: Internal Server Error". Has anyone expe

[galaxy-user] Galaxy @ ISMB/ECCB, 3DSIG, and BOSC

2011-07-12 Thread Dave Clements
Hello all, Galaxy will have a large presence at ISMB/ECCB, 3DSIG, and BOSC, all of which start this week in Vienna. Galaxy related content includes (at least): 1 Galaxy organized workshop on "Genomics for Non-Model Organisms" featuring 4 talks, 7 additional talks at ISMB/ECCB and BOSC, and

Re: [galaxy-user] Workflow API

2011-07-12 Thread Dannon Baker
> My question is how I can modify the script to accept multiple inputs (i.e. > how do I define which files in the input folder I want to be each input) and > if there's a way to specify runtime parameters. For instance, the workflow I > want to execute has a filter step on a tabular input item a

Re: [galaxy-user] exporting HTML with associated files

2011-07-12 Thread Kanwei Li
Hi Joern, I believe this is caused by the bug of extra_files of shared items having the wrong path. It would be fixed in the upcoming week. Thanks, K On Tue, Jul 12, 2011 at 5:38 AM, Joern Toedling wrote: > Hello, > > I have a question regarding exporting data from Galaxy. I have written a > t

[galaxy-user] finding open reading frames and corresponding genes

2011-07-12 Thread Joanne Rampersad
Hi I am sequencing a bacterial genome and have assembled my Illumina reads (40 bp single) using bowtie with a reference genome. This generated a sam file. I would like to obtain a listing of the open reading frames from the bacterial genome and the corresponding genes that they are most similar to.

Re: [galaxy-user] Hi

2011-07-12 Thread Ido Tamir
On Jul 11, 2011, at 10:04 AM, YOGESH OSTWAL wrote: > thanks a lot. > > Sorry for disturbing you again. > > Before starting with the actual data, can I try this analysis with already > available IP and input files of datasets of illumina from NGS repository? why shouldn't you? select something

[galaxy-user] Exome anylisis by Galaxy

2011-07-12 Thread Eduardo Calpena
Hello everyone, I am a new user of Galaxy. I have received the data from an exome of 4 samples. I have two reads from each sample. I have seen the Live Quickies, and I have a general idea that I want to do. I want to find every change in the exome of these samples. Then apply a filter to disc

[galaxy-user] exporting HTML with associated files

2011-07-12 Thread Joern Toedling
Hello, I have a question regarding exporting data from Galaxy. I have written a tool which creates an HTML page and an associated directory containing pictures and text files. However, if I want to export or share the result files, only the resulting HTML is shared/exported and not the associ