April 2013 - galaxy-user - lists.galaxyproject.org

cufflink workflow
by Ianiri, Giuseppe 16 Apr '13

16 Apr '13

Hi, I want to compare gene deferentially expressed in two conditions (1 and 2). I don't have a GTF reference annotation. In my first attempt, I mapped my Illumina reads with TopHat. Then I run Cufflink, and Cuffmerge on my Cufflink outputs for the conditions 1 and 2. At the end, I run Cuffdiff using the Cuffmerge output (1 + 2) and the TopHat output for the two samples of interest. I got genes and transcripts differentially expressed, but I was expecting a quite different output (based on the literature). Do you guys think I did anything wrong? Also, I am not sure the question makes sense, but is the Cuffmerge step essential for the comparison of my two samples? Or could I use my Cufflink outputs for samples 1 and 2 for running Cuffdiff? Regards, Giuseppe Ianiri Email: ianirig(a)umkc.edu

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Metagenome Analysis
by Mike Dyall-Smith 16 Apr '13

16 Apr '13

I have looked through the metagenome tools and looked at the tutorials, and was wondering how one could pull out reads that contain specific protein domains or COGS. Blastx is not possible (?) but megablast could get GI codes, and these could potentially be used to retrieve CDD information. I just can't see the way to do this on galaxy. Any suggestions would be greatly appreciated. Mike DS Sent from my iPhone4

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Re: [galaxy-user] FW: problem using Depth of Coverage (GATK)
by Jennifer Jackson 15 Apr '13

15 Apr '13

Hi Gema, The histogram tool has the columns labeled on the tool's form - there are a few different values that you could pull out and graph, using others as labels, but last one is the coverage for that region of the chrom. The second tool's output is a bedGraph file, the format is also defined on the tool form, with the last value being coverage, the full specification is also here: http://wiki.galaxyproject.org/Learn/Datatypes#BedGraph The tool group "Graph/Display Data" maybe of interest, or you could use a browser to visualize the bedGraph file. The resulting dataset will have links. Best, Jen Galaxy team On 4/12/13 7:20 AM, Gema Sanz Santos wrote: > Hi Jennifer, > > Thank you very much for your answer. > > I think that alternative is good for me, but how can I get the plot? > The output is a table but I don't know exactly which columns to select > for getting the histogram plot or the bed graph. > > Best, > Gema > > From: Jennifer Jackson <jen(a)bx.psu.edu <mailto:jen@bx.psu.edu>> > Date: Tuesday, April 9, 2013 10:50 PM > To: Gema Sanz Santos <ge2sasag(a)gmail.com <mailto:ge2sasag@gmail.com>> > Cc: <galaxy-user(a)lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>> > Subject: Re: [galaxy-user] problem using Depth of Coverage (GATK) > > Hello Gema, > > The tool group "GATK-Tools (beta)" is not indexed to function with the > hg19 genome. > > As an alternative on the public Main Galaxy server, please see the > tool group " BEDTools". There are two tools here that calculate > coverage using BAM data as input. > > Another alternative is to set up either a local or cloud Galaxy, > obtain the hg19 indexes from GATK, then run the analysis there. If you > wish to try this please see: > http://getgalaxy.org > http://usegalaxy.org/cloud > > Take care, > > Jen > Galaxy team > > On 4/7/13 11:41 PM, Gema Sanz wrote: >> >> Hello, I´m trying to use depth of coverage to check the coverage of >> my reads. I already have the bam files (created with sam to bam) but >> they are still not recognized by depth of coverage and I got this >> error message: >> >> "Sequences are not currently available for the specified build" >> >> I used "human (homo sapiens) hg19 full" for mapping but I can´t >> select it, it only allows b37 version. I tried to change the build in >> edit parameters to b37 and then it is recognized but I got another >> error at the end of the analysis. >> >> Any suggestions? >> >> Thank you very much in advance >> >> Gema >> >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Which "Library Type" should I use for single-end reads
by Du, Jianguang 15 Apr '13

15 Apr '13

Hi All, I have a very basic question about parameters for running TopHat. I have datasets of single-end reads. These datasets were generated with Illumina Genome Analyzer IIx. Which "Library Type" should I choose to run Tophat? Thanks. Best, Jianguang

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Barcode splitter on paired end reads
by Veranja Liyanapathirana 14 Apr '13

14 Apr '13

Dear Galaxy team, I am sorry for repeatedly asking this question but I would like some feed back from anyone who has used barcode splitter on paired end reads as the different alternatives I used do not give satisfactory results in terms of expected read alignments. I have a set of Illumina Miseq reads with inhouse barcodes that I need to de maultiplex. It is esstential to make sure that the read 1 and read 2 are split to the same group and in instances that this condition is not fulfilled, the reads to be discarded. I tried to 1. Join read 1 and read 2 and then run barcode splitter, followed by FASTQ splitter 2. Use barcode splitter on read 1 and read 2 separately and use FASTQ joiner on the results to exclude instances where R1 and R2 are in different reads followed 3. Use barcode splitter on R1 and R2 results and straightaway use Bowtie for illumina for mapping The results I get in the three methods are not compatible with each other. I would like to know the best method from the experience of other users on what the best method using Barcode splitter on Illumina Paired end reads, Thank you, Kind Regards, Veranja Veranja Liyanapathirana Graduate Student CUHK

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Tool for changes in bedgraph files
by Kristin Denise Kernohan 12 Apr '13

12 Apr '13

Hi everyone, I am new to Galaxy and wondering if anyone can help me with a quick question. I have two data sets which are currently in a bedgraph format. I am looking for a tool to compare between them and find unique or changed sites. Is there a tool to compare between samples and generate a list of changed sites? Thank you very much Kristin

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Prolonged - Job waiting to run
by Veranja Liyanapathirana 12 Apr '13

12 Apr '13

Dear Galaxy team, I am running short read alignments with Bowtie for illumina using some data generated from split data using barcode splitter. The alignment programme has been indicated the "job waiting to run" status for nearly over an hour. I can meanwhile perform other functions such as data uploading and trimming, splitting etc where the job is continued and completed. Thank you, Kind regards, Veranja Veranja Liyanapathirana, Graduate Student, CUHK

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min alignement count
by Davide Degli Esposti 12 Apr '13

12 Apr '13

Dear Galaxy team, I am performing a differential expression analysis with a cufflinks-cuffmerge-cuffdiff workflow. I was wondering if the default value of 10 fragments for min alignment count is intended to exclude from the significance test all the loci under 10 counts across all samples or if the counts are 10 for at least one sample the test is performed? I thank you for your help Best regards 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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problem with GenomeSpace Exporter
by Gema Sanz Santos 12 Apr '13

12 Apr '13

Dear all, I'm trying to send some data from Galaxy to GenomeSpace, so I can work with this data in Cistrome but I always got this error: GURU MEDITATION: #57662f6109d0460791fa7122116f80ce Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. Could you please indicate me what to do? Thank you in advance Regards, Gema

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Internal Server Error and slow to refresh History
by Gene Genome 11 Apr '13

11 Apr '13

Hi All, When I tried to download the filtered datasets from my History at Galaxy to my computer, I always got this error information: "Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. If you want to contact us about this error, please reference the following GURU MEDITATION: #8aa15caba14d4a3e85ce7ab069" What is the cause for this problem? In addition, It takes about 3 to 5 minutes to refresh my Histories or to view different Histories. However, it is very quick to refresh "Saved Histories". Is it normal? Thanks. Best, Jianguang

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