- galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] Names for genes in RNA-Seq analysis (Emilie Chautard)
by Emilie Chautard 29 Nov '11

29 Nov '11

Hi Olivier, Did you try to run Cuffcompare (part of Cufflinks) on your results? According to the Cufflinks manual (http://cufflinks.cbcb.umd.edu/manual.html ): >Cufflinks includes a program that you can use to help analyze the transfrags you assemble. The program cuffcompare helps you: > - Compare your assembled transcripts to a reference annotation > [...] In the Galaxy version of Cuffcompare, I think that you can provide a reference annotation file using "Use Reference Annotation:", which will be compared to your results with Cufflinks. It makes an "union" of the transcripts obtained with Cufflinks with the annotation file (both in *.gtf format). You can then obtain a transcript identifier for those already annotated. It also provides a class code for the transcripts, which can inform about a potential isoform for example. Hope this helps. Emilie -- Emilie Chautard, PhD Postdoctoral Fellow Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8518 Toll-free: 1-866-678-6427 www.oicr.on.ca > Message: 7 > Date: Thu, 20 Oct 2011 15:12:45 +0200 > From: GANDRILLON OLIVIER <olivier.gandrillon(a)univ-lyon1.fr> > To: "galaxy-user(a)bx.psu.edu" <galaxy-user(a)bx.psu.edu> > Subject: [galaxy-user] Names for genes in RNA-Seq analysis > Message-ID: <CAC5EAED.8E99%olivier.gandrillon(a)univ-lyon1.fr> > Content-Type: text/plain; charset="windows-1252" > > Hello > > I am using Galaxy to analyse RNA-seq libraries made from chicken cells. > > I just groomed my sequences, passed them through TopHat and then Cufflinks. > > This worked well and in the end I get a list of genes and their respective > FPKM values. > > My only problem is that the names of the genes do not appears in the > listing, they are simply reference as "CUFF.1, CUFF.2, " etc? > > Could you please tell me how I could obtain gene names? (I went through the > FAQ and could not get the answer). > > Sincerely > > Olivier >

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'Draw quality score Boxplot' error
by Caroline Proux 29 Nov '11

29 Nov '11

Hi, I have illumina ChipSeq data and I want to use the "Draw quality score Boxplot" I run the"quality format converter (ASCII numeric)". But the "Draw quality score Boxplot" do an error "An error occurred running this job:Could not find/open font when opening font "arial", .." where is my problem? thank you so much Caroline Proux

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barcode splitter and clustering analyses?
by Simon Bulman 28 Nov '11

28 Nov '11

Dear Galaxy we have a 454 metagenomic dataset. We have used barcode splitter to divide the dataset into it's constituent amplicons. We have also been using a clustering application (dnaclust) in Galaxy to subdivide the dataset by similarity. My question is; are there Galaxy tools to allow the combining, sorting and counting of these two outputs? For example, can each cluster - and then each sequence within that cluster - be given an identifier.... so that one can then split the output by barcode and summarise the data along the lines of amplicon/barcode X has X number of sequences within cluster 1, X number of sequences within cluster 2, ... etc? Am I making any sense? This is the sort of problem that sounds like it is solvable in Excel and, indeed, a UK colleague of mine has been doing just this. But is there a straightforward means to do so in Galaxy? It is not obvious to me in the Filtering or Sorting tools. best wishes Simon The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.

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An update to Galaxy CloudMan
by Enis Afgan 28 Nov '11

28 Nov '11

A new version of CloudMan for running Galaxy on Amazon cloud has been released today. Any new cluster will automatically use this version. Existing clusters will have a link displayed at the top of the CloudMan console offering to perform an automated update. The new version brings the following updates/features: - Added ability to specify a path where Galaxy is installed as part of user data (using galaxy_home key). This allows custom Galaxy application to be installed and picked up by CloudMan instead of the default one. This works across cluster invocations as well as for shared clusters. For a complete list of user data options see http://wiki.g2.bx.psu.edu/Admin/Cloud/UserData - Use /etc/profile instead of /etc/bash.bashrc for system wide shell logins - Support for 3.0 Kernel on Ubuntu 11.10 for SGE. Contributed by Brad Chapman. - Fix for SGE install after cloud-init has run and changed /etc/hosts - post_start_service now runs if the script exists in the cluster bucket even if no URL was provided as part of current user data - Fix recognition of existing and attached file system volumes on instance reboot

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Question regarding: FASTQ Quality Trimmer
by Rahul Kanwar 28 Nov '11

28 Nov '11

Hello, I am running Galaxy locally and it has been performing flawlessly! I wanted to get more insight about this flag in the FASTQ Quality Trimmer program: Maximum number of bases to exclude from the window during aggregation Does it mean the number of 5' bases to exclude while the doing the trimming step [i.e. the sliding window starts this many bp after the read start] ? I would really appreciate if someone could shed more light on this. Thanks. regards, Rahul

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Unable to run SICER or Find Peaks
by Anupam Paliwal 28 Nov '11

28 Nov '11

Hi, I want to use SICER or Find Peaks for peak calling on GALAXY. I am using my aligned ChIP-seq tag .BAM files. However for both the tools the history is unable to pick the Bowtie-ligned SAM to BAM converted files. On the other hand, using MACS the same files are working nicely for peak calling. Thanks, AP

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Error running tool
by Toqa Manasrah 25 Nov '11

25 Nov '11

Hello everybody, I am trying to run my tool Vispa but every time i try to i got this error messages: An error occurred running this job: /home/galaxy/galaxy-dist/tools/vispa/main.bash: line 13: ./parser_v.2.sh: No such file or directory /home/galaxy/galaxy-dist/tools/vispa/main.bash: line 16: ./vispa.bash: No such file or directory although all these files are reside under the same directory and have the permission 755. how can I solve the problem? Thanks and regards, Tuqa.

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Galaxy Upload tool
by Toqa Manasrah 24 Nov '11

24 Nov '11

Hi everybody, I am integrating my own tool with galaxy. the command to run is: ./main.bash <readFile> <referenceFile> threads n t > <log> & the input files read and reference are of type fasta. threads, t and n are integers. log is to prevent console outputs. should I load these files from the page which run the command. or i have to use the Galaxy upload tool. and how? on the other hand. the output is implied and should be on the same directory where the source files. Thank you so much. Tuqa.

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Upload executable in galaxy
by Giota Kottara 23 Nov '11

23 Nov '11

Dear galaxy developers, I am trying to integrate an executable tool in a private instance of galaxy. I stored the configuration .xml file and the executable in tools folder of Galaxy and the tool appears in the homepage. Nevertheless when i am running the tool it doesn't seem to find the executable. Am I forgetting something? Thank you in advanceGiota Kottara

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Galaxy test won't run a bwa job
by Carlos Borroto 22 Nov '11

22 Nov '11

Hi, I'm trying to test a workflow using tools only available on the test server, for this I have uploaded a limited subset of my data that should run fairly quickly. The first step is a BWA mapping, but the job has being in the queue since yesterday. Is it fine to run this kind of test there? Thanks, Carlos

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