August 2011 - galaxy-user - lists.galaxyproject.org

aaChanges
by David Joly 30 Aug '11

30 Aug '11

Hi everybody, Maybe a dumb question but does someone know if we can use the aaChanges tool on a custom genome? I have my SNP dataset and my gene dataset but I can only assign them to one of the genome build already in UCSC... I am using the web server of galaxy. Do I need to install my own local instance of Galaxy in order to add a custom genome build? Thanks, David

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rna-seq mutation detection
by Richard Mark White 30 Aug '11

30 Aug '11

Hi, I am trying to look at differences between two RNA-seq samples to see if there are mutations in one of them relative to the other (i.e. not in comparison to a reference genome). Does anyone know of a way to do this within galaxy? Any help is appreciated! rich

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Galaxy is Hiring
by Dave Clements 29 Aug '11

29 Aug '11

Hello all The Galaxy Project is growing and has open positions in both the Penn State and Emory groups (http://wiki.g2.bx.psu.edu/News/Galaxy%20is%20Hiring) *Penn State: System administrators/analysts* The Nekrutenko Lab <http://www.bx.psu.edu/%7Eanton/> at the Huck Institutes of Life Sciences <http://www.huck.psu.edu/> at Penn State <http://psu.edu/>is currently recruiting system analysts/administrators with experience in building and maintaining complex performance compute environments. The areas of immediate need include: - Storage balancing and tiered storage - Virtualization - Schedulers - Deployment of Galaxy instances and dependence management - Relational databases and query optimization - User management A minimum of 5 year experience with UNIX/Linux system administration is required. Applicants should submit a CV and list of references to jobs(a)galaxyproject.org. <http://bx.mathcs.emory.edu/joining/> *Emory: Software Engineers and Post-Docs* The Taylor Lab <http://bx.mathcs.emory.edu/> in the Biology<http://www.biology.emory.edu/>and Mathematics & Computer Science <http://www.mathcs.emory.edu/> at Emory University<http://emory.edu/>is looking for software engineers <http://bx.mathcs.emory.edu/joining/sw/> and postdoctoral scholars<http://bx.mathcs.emory.edu/joining/postdocs/>to work on the Galaxy project. We are seeking software engineers <http://bx.mathcs.emory.edu/joining/sw/>with expertise in distributed computing and systems programming, web-based visualization and visual analytics, informatics and data analysis and integration, and bioinformatics application areas such as re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. These are full time positions located in Atlanta, GA. See the official posting<http://bx.mathcs.emory.edu/joining/sw/>for full details. Postdoctoral applicants <http://bx.mathcs.emory.edu/joining/postdocs/>should have expertise in Bioinformatics and Computational Biology and research interests that complement but extend the lab's current interests<http://bx.mathcs.emory.edu/research/>: The Galaxy project; distributed and high-performance computing for data intensive science; vertebrate functional genomics; and genomics and epigenomic mechanisms of gene regulation, the role of transcription factors and chromatin structure in global gene expression, development, and differentiation. See the announcement<http://bx.mathcs.emory.edu/joining/postdocs/>for full details. If any of these positions describe you then please consider applying. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Cufflinks quartile normalization
by David Joly 27 Aug '11

27 Aug '11

Can someone help me understanding the quartile normalization in Cufflinks? I read different threads in which they reported that the FPKM values were inflated after normalization (-N) but most people didn't report their values so I don't know how big the inflation should be... In my case, the difference is huge! The FPKM values for the four first genes without normalization are in the range of [61 - 184] while after normalization, they are in the range of [2.4e+6 - 7.4e+6]. Even though this inflation does not seem to affect the calculation of the gene expression changes [ log (FPKM2/FPKM1) ], I'm wondering if something is wrong with my dataset. Is it was I should expect? Is it always better to use the normalization? Thanks, David

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load data from galaxy to IGV
by Jennifer Jackson 27 Aug '11

27 Aug '11

Hi Jen, is anyway I can directly load the analyzed data from galaxy to IGV (Integrative genome viewer) without downloading data to my computer first? Thanks, tao

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Error when running Generate Pileup
by Alison Gardner 26 Aug '11

26 Aug '11

Hello, I am aligning Illumina paired end sequence using BWA, then run SAM-to-BAM resulting in a 1.1 Gb file. But when I then generate pileup on this file column 4 (consensus bases) are all N's and the file is now 8.4 Gb. Can someone tell me what might be going on? Any help much appreciated. Thanks Alison Gardner Neurogenetics Research Program, SA Pathology (at Women's and Children's Hospital), Level 9, Clarence Rieger Bldg., 72 King William Road, North Adelaide, S.A., Australia, 5006

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galaxy with cuffdiff output
by 姚晨 26 Aug '11

26 Aug '11

Dear all, I use cuffdiff in galaxy net version. The output are isoform.diff , gene.diff ...etc, but I want to find the differential expressed non-coding RNAs. How can I get these information? Thank you Chen Yao

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line estimation for pileup generation
by Austin Paul 25 Aug '11

25 Aug '11

Hello, I am curious if the line estimation shown in the history window for pileup generation is at all accurate. I am using the pileup files to generate expression data from bwa mapping for looking at differential expression, but I am having some trouble understanding the line estimates. For example, for one pileup file, when I cut the reference id column and the number of hits column (columns 1 and 4), the number of lines in the cut file is about 25% that of the pileup file, and for another file it will be 5000%. How can the number of lines grow 50x when I am just cutting columns from the file? Shouldnt the line estimate be the same? Thanks, Austin

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Update: Cuffdiff question about using an unspecified (?) database/build
by Jennifer Jackson 25 Aug '11

25 Aug '11

cross-post ===> Please use "Reply All" when responding to this email! <=== -------- Original Message -------- Subject: Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build Date: Thu, 25 Aug 2011 08:41:21 -0700 From: Jennifer Jackson <jen(a)bx.psu.edu> To: Robert Curtis Hendrickson <curtish(a)uab.edu> CC: 'galaxy-dev(a)lists.bx.psu.edu' <galaxy-dev(a)lists.bx.psu.edu>, David K Crossman <dkcrossm(a)uab.edu> Hi Curtis, Changeset details: http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9 We are planning on releasing a distribution within a week, so alternatively you could wait and pull from there, if you normally work from the galaxy-dist repository. And for everyone tracking this fix: the changeset was applied to the public Galaxy main instance yesterday (http://usegalaxy.org) Hope this helps! Jen Galaxy team On 8/25/11 7:55 AM, Robert Curtis Hendrickson wrote: > Jen, > > Can you also please describe the details of the fix? > We need to fix the same issue in our local instance, but don't know if this was a fix to cuffdiff, or to galaxy. Which one should we be updating? > > Regards, > Curtis > > >> -----Original Message----- >> From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user- >> bounces(a)lists.bx.psu.edu] On Behalf Of David K Crossman >> Sent: Friday, August 19, 2011 11:10 AM >> To: Jennifer Jackson >> Cc: galaxy-user (galaxy-user(a)lists.bx.psu.edu) >> Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) >> database/build >> >> Jen, >> >> Thank you very much for the reply. I'm glad to know it is a known bug >> and not something on my side of things. So, would my analysis be affected if >> I did change the bam file "Database/Build" to the older tree shrew version >> found in the drop down list? What significance does this "Database/Build" box >> have in downstream analysis if you have your own fasta reference genome file >> and gtf annotation file that is being referenced instead of a locally cached >> one? I'm just trying to obtain a better understanding of the "Database/Build" >> box for analyses where I provide the fasta and gtf file. >> >> Thanks, >> David >> >> >> -----Original Message----- >> From: Jennifer Jackson [mailto:jen@bx.psu.edu] >> Sent: Friday, August 19, 2011 9:20 AM >> To: David K Crossman >> Cc: galaxy-user (galaxy-user(a)lists.bx.psu.edu) >> Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) >> database/build >> >> Hello David, >> >> This is a known bug. The correction is planned to be moved out onto the public >> Galaxy instance at the next update (within a week). >> >> Sorry for the current inconvenience, >> >> Best, >> >> Jen >> Galaxy team >> >> On 8/19/11 7:00 AM, David K Crossman wrote: >>> Hello! >>> >>> I have an RNA-Seq project which consists of 5 samples from the species >>> tree shrew. When uploading these fastq files into Galaxy, I chose >>> "unspecified (?)" for the database/build since the latest tree shrew >>> version is not in the drop down list. When using TopHat, >>> Cufflinks/Compare I have selected a reference genome from my history >>> instead of using a built-in index, as well as a gtf annotation file >>> for Cufflinks/Compare and everything has been working fine. Now, I am >>> at the Cuffdiff step and I am running into an error when setting it up >>> to perform replicate analysis. When I select my TopHat accepted hits >>> bam file I see a red X and the error: "Unspecified genome build, click >>> the pencil icon in the history item to set the genome build." Here's a >>> screenshot of what I'm seeing: >>> >>> Since the latest reference genome for tree shrew wasn't listed, that's >>> why I chose "unspecified (?)." Should I go back and edit these >>> accepted hits bam files to say the Database/Build from the drop down >>> list is "Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)?" I know that >>> this is simple to change, but will this affect my results in any way? >>> Any help/info would be greatly appreciated. >>> >>> Thanks, >>> >>> David >>> >>> >>> >>> ___________________________________________________________ >>> 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/ >> >> -- >> Jennifer Jackson >> http://usegalaxy.org >> http://galaxyproject.org/Support >> >> ___________________________________________________________ >> 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/ > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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output of cuffdiff in galaxy
by chenyao.bioinfor＠gmail.com 25 Aug '11

25 Aug '11

Dear all, I use cuffdiff in galaxy net version. The output are isoform.diff , gene.diff ...etc, but I want to find the differential expressed non-coding RNAs. How can I get these information? Thank you Chen Yao

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