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Call for papers for a special GCC2013 and Galaxy series in GigaScience
by Dave Clements 04 Apr '13

04 Apr '13

Hello all, I am pleased to inform you that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience* and that BGI will generously cover the article processing fees for these articles. See the announcement below for details. thanks, Dave C -------------------------------- The 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> and BioMed Central <http://www.biomedcentral.com/> are announcing a special thematic series in *GigaScience <http://www.gigasciencejournal.com/> *, a new journal co-published in collaboration between BGI Shenzhen<http://www.genomics.cn/en/index> and BioMed Central <http://www.biomedcentral.com/> focused on studies utilizing large-scale datasets and workflows. Galaxy<http://galaxyproject.org/> is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses. All accepted oral presentations from the meeting will be eligible for consideration in the series, and working with the scientific committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Scientific_Committee>, peer review will be coordinated, thorough and timely. BGI has been generously covering the open-access article-processing charges<http://www.gigasciencejournal.com/about/apcfaq> for the journal’s launch, and this offer will be extended to all submissions from the 2013 conference. Covering the themes of the conference, discussion and research is considered highlighting best practice for local Galaxy installation, management and use, as well as interesting tools, data sources, or novel uses of Galaxy. Addressing many of the goals of Galaxy to enable more accessible, reproducible, and transparent genomic science, submissions can utilize a novel format, where all of the workflows, tools and supporting data can be hosted and integrated into accepted papers using independently citable digital object identifiers<http://en.wikipedia.org/wiki/Digital_object_identifier> from the journal's Giga-Galaxy server <http://galaxy.cbiit.cuhk.edu.hk/> and GigaDB database <http://gigadb.org/>. Please contact the conference organizers <gcc2013-sci(a)galaxyproject.org> or GigaScience editors <editorial(a)gigasciencejournal.com> for further information, or submit a manuscript<http://www.gigasciencejournal.com/authors/instructions/research> or conference abstract<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts>, mentioning you would like to be considered in the series. The deadline for consideration for oral presentations to the meeting is 12th April, but later submissions for exceptional poster presentations (deadline 3rd May) and related work utilizing Galaxy may also be considered for the open series<http://www.gigasciencejournal.com/series> . Scott Edmunds Executive Editor *GigaScience <http://www.gigasciencejournal.com/>* -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Extracting sequences for transcripts from reference genome
by Lizex Husselmann 04 Apr '13

04 Apr '13

Dear Galaxy community I'm new to galaxy and would like to ask the following: I have trimmed, QC'ed my data received from Illumina HiScan SQ, paired and single end data. Mapped using Tophat, run cufflinks, cuffmerge and cuffdiff. I would like to analyze the gene_exp.diff file by extracting the significant transcripts. I've used grep "yes" to extract only the significant transcripts. From this info I have the locus start and end coordinates of each transcript for example "XLOC_000544 XLOC_000544 - chr1:12763969-12765675 C0 C4 OK 3.16487 1628.25 9.00696 -4.57022 4.8722e-06 0.00905256 yes". How can I go about to extract this information/or sequence from the reference genome. Kind regards Lizex 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 000 604 Fax number : 0800 00 7788 Email address : arc(a)tip-offs.com Please Call me : 32840 Website: www.tip-offs.com For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.

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Phyloviz and problem viewing nexus and newick files
by Yvan Le Bras 03 Apr '13

03 Apr '13

Dear Galaxy users, I'm trying to view files from phylogenetics analyses in Newick or nexus formats. It seems that Phyloviz doesn't work since the last update of Galaxy. Can you inform me about this problem and the possibility to make Phyloviz working on a local instance? When I try on the main galaxy instance, I have the following error number: GURU MEDITATION: #1a7e2c6048fd4852ae09587cba0a09e8 Thank you very much for your help. Best Regards, Yvan -- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Yvan Le Bras, PhD <°))))>< e-Biogenouest project http://www.e-biogenouest.org CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex yvan.le_bras(a)irisa.fr

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Change format with "edit attributes"
by Gema Sanz Santos 03 Apr '13

03 Apr '13

Hello, I'm trying to change the format to the output files from Barcode splitter from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read that it can be done through the edit attributes, I go to datatype and select fastaq, save and then go to convert format and press convert but the resulting file is 0 bytes and is not recognized by Bowtie. I´ve also tried to upload by copying the link and selecting fastaq as format but in this case, I got the file shown in the picture and it is not recognized by Bowtie again. What can I do?? I don´t know how to continue because I´m not able to change the format to fastaq! Thank you very much for your help in advance Best, Gema

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April 2013 Galaxy Update
by Dave Clements 02 Apr '13

02 Apr '13

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Galaxy April 1, 2013 Distribution
by Jennifer Jackson 02 Apr '13

02 Apr '13

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GCC2013 Oral Presentation Abstract Submission Closes 12 April
by Dave Clements 01 Apr '13

01 Apr '13

Hello all, This is just a reminder that the *deadline for submitting an oral presentation abstract is 12 April, which is less than two weeks away*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. Thanks, Dave C On Sun, Feb 24, 2013 at 7:40 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Dear Galaxy Community, > > We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are > now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> > . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University > of Oslo <http://uio.no/>. > > GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity > to participate in two full days of presentations, discussions, poster > sessions, keynotes, lightning talks and breakouts, all about > high-throughput biology and the tools that support it. The conference also > includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for > the second year in a row, this year with more in-depth topic coverage, more > concurrent sessions, and more topics. > > If you are a biologist or bioinformatician performing or enabling > high-throughput biological research, then please consider attending. > GCC2013 is aimed at: > > - Bioinformatics tool developers and data providers > - Workflow developers and power bioinformatics users > - Sequencing and Bioinformatics core staff > - Data archival and analysis reproducibility specialists > > *Early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + > main meeting) starting at ~ €95 for post-docs and students. Registering > early also assures you a spot in the Training Day workshops you want to > attend. Once a Training Day session becomes full, it will be closed to new > registrations. Early registration closes 24 May. > > *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> > * for oral presentations closes 12 April, and for posters on 3 May. > Please consider presenting your work. If you are working with big > biological data, then the people at this meeting want to hear about your > work. > > Thanks, and hope to see you in Oslo! > > The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> > > PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> > ! > -- > http://galaxyproject.org/GCC2013 > <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Uploading Illumina BAM files in Galaxy
by Priya Bhatt 28 Mar '13

28 Mar '13

Dear Galaxy Users, I had a quick question as a new Galaxy user. I just received WGS data from Illumina where I'm given .bam files. I am not given .fastq files. Most of the Galaxy tutorials I've seen online have started with raw data in .fastq format. Can Galaxy handle if I were to upload a .bam file using the "Get Data" tool? Furthermore are there any examples/workflows available that others have created when using Illumina data Thank you! Best, Priya

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downloads MAF files
by Navin Rustagi 28 Mar '13

28 Mar '13

Hi, I want to download MAF files for the exonic regions of the genome. Additionally I want the sequences to be in phase as well. How does one do that. Regards, Navin

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Depth command in SAM tools
by Els Willems 27 Mar '13

27 Mar '13

Dear all, I am a Phd student working on chicken genomics, with limited experience in the bio-informatics field. I performed an RNA-Seq experiment with single end 50 bp reads to find differential gene expressions between different groups. I have mapped this data with Tophat and used flagstat and Picard to check the number of mapped reads. To check the coverage of my genome, I could use the number of mapped reads and multiply this by the read length and divide by the genome size, but of course since I used mRNA as input material, average coverage will be low (only exons presents). I would like to use the Samtools Depth (as I read on SeqAnswers) to get the average coverage for a coveraged base AND the total base coverage, but this does not seem to be included in Galaxy. Does anyone know a way around this? Other useful tips and tricks are also welcomed. Thank you very much. Have a nice day. Yours Sincerely, Els --- Ir. Els Willems KU Leuven Department of Biosystems Division Livestock - Nutrition - Quality Laboratory of Livestock Physiology Kasteelpark Arenberg 30 bus 2456 B - 3001 Heverlee T (+32) 016 32 17 29 F (+32) 016 32 19 94

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