- galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] [galaxy-dev] extract DNA sequences
by Jeremy Goecks 31 Jan '13

31 Jan '13

Hello, > However, this is not working here. Can you be more specific about what's not working? If the tool failed, please feel free to report the bug using the "bug" icon. > How > do I specify that the strands I am extracting are in the fasta file in my account in Galaxy? GFF requires a strand column, and the tool will automatically use this data to extract sequence data. > Should I be using another tool, please? This is the correct tool. Finally, questions about using Galaxy and its tools are best directed to the galaxy-user mailing list, so I've moved your question to that list. Best, J.

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does Galaxy have a tool for converting .sra files to fastq files?
by Elwood Linney 31 Jan '13

31 Jan '13

Hello, I would like to download some GEO files that complement my own research with zebrafish embryos but apparently GEO is now only providing .sra flles. For a not very experienced unix person, does Galaxy have a tool for this or is there a clear description somewhere else of how to do it for someone who is not a bioinformaticist? Thanks, el linney Duke University Medical Center

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running time of Cufflinks on main Galaxy
by Davide Degli Esposti 31 Jan '13

31 Jan '13

Dear Galaxy team, in the last two days I am trying to run Cufflinks on some sam files, but the work is kept in queue. Actually I performed cufflinks on the same files some times ago, but with different parameters and it worked after some hours. Is this a problem due to my new parameters or are the servers currently overused? Thank you for your help Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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Converting files to gd_snp format
by Sheehan, Michael - (michaelsheehan) 30 Jan '13

30 Jan '13

I would like to convert VCF files to gd_snp format to be used in some population genomic analyses. A tutorial online makes it seem like this is the correct path to follow to conduct such analyses: http://www.bx.psu.edu/~giardine/tutorials/example2/part1/snpTable.html I have been using Galaxy on the free public server and this tools does not appear to be present anywhere. Does anyone know where the tool has gone or is there a way to add the needed tools back? Thanks Mike

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Mapping miRNA data
by Mark Lindsay 29 Jan '13

29 Jan '13

Dear All I am interested in using Galaxy to compare miRNA sequencing data. I have previously groomed, clipped and then mapped miRNA data onto hg19 using bowtie. I have then identified differentially expressed miRNAs using cuffdiff and the UCSC downloaded miRNA/snoRNA database. However, I have recently tried to repeat this process but find the cuffdiff is unable to run. I just wondered why cuffdiff is no longer working or if there is alternative approach to comparing miRNA expression? Best wishes Mark

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How to determine differentially expressed genes using Galaxy?
by Ben Ben 29 Jan '13

29 Jan '13

Hi All, Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differentially expressed transcripts from read alignments)? Any alternative? As far as I know, *Penn State Version* doesn't integrate the DESeq function. * And Cuffdiff seems stop working in Penn State * Thanks very much for the response!! Best wishes,

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reference annotation for whole transcriptome RNA-Seq
by Davide Degli Esposti 29 Jan '13

29 Jan '13

Dear all, I am trying to get an exhaustive reference annotation for RNA-Seq analysis. I was thinking that the patched GTF annotation files for cufflinks Jeremy indicates in RNA-Seq step by step tutorial should be fine for me, but I am not able to find on the Shared data > Data libraries. Have they been replaced by iGenomes annotations? I thank you for your help Best regards Davide----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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How to run DESeq? Please Help.
by Ben Ben 28 Jan '13

28 Jan '13

Hi All, Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differentially expressed transcripts from read alignments)? As far as I know, *Penn State Version* doesn't integrate the DESeq function. Thanks a lot for any response!! Best wishes, Ben

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2013 Galaxy Community Conference (GCC2013) Training Day: Please vote!
by Dave Clements 28 Jan '13

28 Jan '13

Hello all, A list of possible topics <http://bit.ly/gcc2013td> for the GCC2013 Training Day <http://bit.ly/gcc2013td> is now available at http://bit.ly/gcc2013td. Please take a few minutes to review these possibilities <http://bit.ly/gcc2013td> and *then vote for your three favorite topics* at http://bit.ly/gcc2013tdpoll* Your votes will determine not only the topics that are offered, but also which topics should be offered more than once, assigned to the larger rooms, and which ones should not be scheduled at the same time. Your vote matters. Once voting closes on 11 February, we will contact possible instructors and publish a Training Day schedule before registration opens on 22 February. *About the GCC2013 Training Day* The 2013 Galaxy Community Conference (GCC2013)<http://galaxyproject.org/GCC2013> will start on 30 June with a Training Day <http://bit.ly/gcc2013td> featuring 4 parallel tracks, each with three workshops, each of which are two hours long, for a total of twelve sessions. There will be at least one complete track (3 consecutive workshops) about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances. As always, please let us know if you have any questions. Thanks, and hope to see you in Oslo! Dave Clements, on behalf of the GCC2013 Organizing Committee * Note: You don't have to vote for exactly three topics. You can vote for fewer topics and have each vote count for more, or you can vote for more topics and have each vote count for less. Links: http://bit.ly/gcc2013td - Training Day possible topics list http://bit.ly/gcc2013tdpoll - Vote! http://galaxyproject.org/GCC2013 - Conference home page http://bit.ly/gcc2013prom - help get the word out -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Moving history datasets to libraries
by Ted Goldstein 27 Jan '13

27 Jan '13

I must be mistaken, but I don't see any way to move a dataset that I create in a history to a library except to download it and upload it again. Can this be correct? It seems like this is essential functionality. Please tell me I am wrong. Thanks, Ted

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