[galaxy-user] Cloudman - Problem starting shared cluster

Hi guys, After launching Cloudman on the Initial Cluster Configuration dialog I selected the "Share-an-Instance Cluster" option and put in this share string: cm-31bf91279e41769ff78af22c1a276ece/shared/2012-01-12--18-03 But after that I see this message in the log: 12:52:19 - Problem copying shar

[galaxy-user] embl 66 genome for RNAseq analysis

Hi, How do I run Tophat and RNA-Seq analysis using the GRCH37- embl 66 genome? I noticed there is no input for this genome version. Can I construct a reference genome from the following embl format source sequences: ftp://ftp.ensembl.org/pub/release-66/embl/homo_sapiens/, and map it against my

Re: [galaxy-user] embl 66 genome for RNAseq analysis

Hello Karthik, Because it is sourced from UCSC, the GRCh37 genome is available in Galaxy as "hg19". The full name is: Human Feb. 2009 (GRCh37/hg19) (hg19) This aligns with how Ensembl also understands the content: http://lists.ensembl.org/pipermail/dev/2012-February/002180.html For RNA-seq an

[galaxy-user] USing GATK DepthOfCoverage with all exon enriched data

Hi, I have NGS results of DNA enriched for exons with an AllExon kit (Agilent). I have a bed file with the list of targeted sequences. I want to use GATK DepthOfCoverage to compare the results to the bed file and to get all the targets that were covered by _

Re: [galaxy-user] USing GATK DepthOfCoverage with all exon enriched data

and another question: My steps were: 1. BWA alignment 2. SAM-to-BAM 3. rmdup. when I'm trying to give 3 (rmdup results) as an input to GATK DepthOfCoverage, an error appears: " Sequences are not currently available for the specified build." What did I do wrong? Many thanks! Lilach 2012/4/2

[galaxy-user] April 2012 Galaxy Update

Hello all, The April 2012 Galaxy Updateis now available. *Galaxy Update * is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complements the *Galaxy Development News

Re: [galaxy-user] Blast2GO local instance Re: Table with gene count reads

On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: > > Have you seen the README file that comes with the > Blast2GO wrapper? Perhaps the 'install from toolshed' > could be tweaked to make this kind of documentation > more visible... > If you are installing a single repository that contains a file

[galaxy-user] Google Summer of Code 2012 - Application Deadline on Friday 6th

The Genome Informatics group , is taking part in the Google Summer of Code (GSoC) program. This year, the Genome Informatics group, will be organizing the joint efforts of Galaxy , GBrowse

Re: [galaxy-user] Cloudman - Problem starting shared cluster

Hi guys, I'm still stuck on this :-(. Are there any log files I could look at to get more details? I'm definitely willing to dive in an get to the bottom of this issue. Can anyone recommend a starting point? Thanks again, Greg On Mon, Apr 2, 2012 at 9:01 AM, mailing list wrote: > Hi guys, >

Re: [galaxy-user] Cloudman - Problem starting shared cluster

The first thing to check would be to verify that that the bucket and contents exist in your account. Use the AWS console to log in, go to the S3 tab, and look for the bucket 'cm-31bf91279e41769ff78af22c1a276ece' and verify the /shared/2012-01-12--18-03 folder structure exists. -Dannon On Apr

[galaxy-user] Generating gff file

Hi, Is it possible to generate gff file in galaxy which I can use in Seqmonk? Abdullah -- Abdullah Al Mahmud, PhD Postdoctoral fellow University of Montreal Lab of Dr. Jacques Michaud CHU Sainte-Justine Research Center, 3175, Cote-Sainte-Catherine, A-709 Montreal, Quebec, H3T 1C5, Canada. abdul

[galaxy-user] Disk space quota Issue

Dear Administartor My disk space quote is full, is their any way to increase it,or only way is delete some files... Best Ateeq   Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau __

[galaxy-user] BWA in Galaxy

Is it possible to align FASTq reads from Illumina Hi-seq reads to human genome in Galaxy? I see only Bowtie/ I guess next question will be how different is Bowtie from BWA? I want to find out sequence variations. Thanks ___ The Galaxy User lis

Re: [galaxy-user] Cloudman - Problem starting shared cluster

Along with the folder structure Dannon is referring to, an appropriate EBS snapshot should exits under your account. This is available from the EC2 tab on the AWS console. As far as the complete logs goes, on CloudMan's admin page, there is a link to the full CloudMan log (alternatively, the same l

Re: [galaxy-user] Training on NGS data analysis

Hi Aarti, The short answer to your question is no. We do provide training on how to use Galaxy to do bioinformatic analysis. See the Events page (http://wiki.g2.bx.psu.edu/Events) for what's coming up. We don't offer training on NGS analysis per se. That is a very complex subject and we current