- galaxy-user - lists.galaxyproject.org

Data gets deleted from public server
by shamsher jagat 08 Nov '11

08 Nov '11

I uploaded two BAM files and was working with them but when I tried to use them again they are automatically deleted along with all the steps of analysis? Any reason or I am missing something. Shamsher

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Cufflink error
by Lizex Husselmann 08 Nov '11

08 Nov '11

Hi I've started an alignment using the command line (Tophat v1.3.3). I've uploaded the files (accepted.bam) onto Galaxy and upon doing the Cufflinks analysis on the Galaxy interface, it shows an error. I had to look at the options. I've change the options to default and run it again but still the same error. Is the accepted.bam file not compatible with the Galaxy Cufflinks? Is there something I not doing? Kind regards Lizex Disclaimer This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:Servicedesk@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 21 20 56 Fax number : 0800 200 796 Email address : fraud(a)kpmg.co.za For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.

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SNPeff tool?
by Laura Elizabeth Spoor 08 Nov '11

08 Nov '11

Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Cuffcompare error
by Alessia D 08 Nov '11

08 Nov '11

Hi, I am trying to run Cuffcompare on a set of 6 Cufflinks-generated datasets (3 replicates of 2 conditions). I am consistently getting the following error: Error running cuffcompare. Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu) Error: no XLocus created for transcript CUFF.34072.1 (file ./input3) [2, 2], on chrY+:274296-277218 However, if I run Cuffcompare on the 2 conditions separately (3x Cufflinks datasets), everything works fine. Does anyone know why this is? Thanks Alessia

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Uploading Genome from Ensembl
by Scroggins, Sheena 08 Nov '11

08 Nov '11

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

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number of concurrent jobs/user
by Petr Novak 08 Nov '11

08 Nov '11

Is it possible to limit number of concurrent jobs when job_runner is pbs? The setting in universe_wsgi.ini is obviously limiting only locally run jobs. Petr

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(no subject)
by Xiangming Ding 06 Nov '11

06 Nov '11

Hi galaxy I am a new user of galaxy. i met a problem and didnot find similar question in FAQ. I wanted to upload the data from DDBJ DRA dataset to galaxy through UTL method. The file is around 800M. However after uploading, the FASTQ file was just around 2M. So I wanted know whether it is possible to upload a large file to galaxy through URL method? or I should download the file to my pc and then uploading to galaxy through FTP method. Thanks xiangmimg

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Bed to Wiggle?
by shamsher jagat 04 Nov '11

04 Nov '11

Is there an option to convert Bed file to wiggle file in Galaxy? Thanks

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BWA install problem
by Christopher Callaway 04 Nov '11

04 Nov '11

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 #2222 Salt Lake City, UT 84108

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Question about Cuffdiff
by Alessia D 04 Nov '11

04 Nov '11

Hi, I am confused about the first line in cuffdiff (using Galaxy on the cloud, not sure if it's different for local instances). It reads: Transcripts:(choose a file)A transcript GTF file produced by cufflinks, cuffcompare, or other source. What file should I load here? I have 4 groups of 2-4 replicates each that I am comparing, and am using the "grouping" option that follows. Should I use one of the files produced by cufflinks? If so, which ones? Or should I rather use the GTF file of RefSeq genes from the UCSC database? Thx!!A

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