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Inconsistency between cufflinks and cuffdiff. This is killing me.
by Jia Meng 18 Jun '12

18 Jun '12

<<Problem>> The cufflinks and cuffdiff results are not consistent with each other. This is killing me. Does it make sense? << Obseration >> We have 3 control samples and 3 treated sample. For many genes, their FPKM in cufflinks and cuffdiff are far from consistent. In cufflinks result, for a gene’s FPKM are control group (sample: 1,2,3)：0， 0， 4.8 treated group(sample: 1,2,3)：0， 0， 6.0 In cuffdiff, the estimated FPKM are control group： 12.6 treated group：2.0 <<Method>> Use ucsc gene annotation gtf file, mm9, downloaded from UCSC table database Use cufflinks on each individual sample. Cufflinks: galaxy mirror at cistrome, minimal count:10, no quantile normalization, use gtf as reference, no background correction Use cufflinks on treated groups (3 biological replicates) and control groups (3 biological replicates) Cuffdiff: galaxy mirror at cistrome, minimal count:10, no normalization, use gtf as reference, no background correction <<Additional Comments>> Cufflinks returns 55350 transcripts, while cuffdiff return 55418 transcripts, even though they use the same gene annotation gtf file. For the 6 cufflinks results (corresponding to 6 samples), the transcript ids are all the same, but the order are not, <<Question>> Does it make sense? Or did I do anything wrong?

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jobs not running on main server
by Jacob Musser 18 Jun '12

18 Jun '12

Hello, I uploaded a couple small files via ftp to do some basic text manipulation on them in the main galaxy server. I have queued up several jobs (including just importing the files I uploaded into a history) but after two hours of waiting they are still gray and "waiting to run." I have been using galaxy regularly lately and have never had to wait very long for a job to start running (usually a matter of seconds). I am not above my quota so this is not the problem. Is there something else I need to do or is there a problem with the servers that would explain why jobs aren't being run? All the best, Jake

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Galaxy main not running jobs..
by Jayaraman, Shyam 18 Jun '12

18 Jun '12

Hi, My username is shyamsundar19489(a)gmail.com Galaxy main is not running jobs since today morning. They stay queued (gray) forever. I deleted and then re queued them twice. Still nothing.. Is the server down or is something wrong with my account?? Kindly advice. Shyam S Jayaraman MD Staff Research Associate Division of Dermatology LABioMed Research Institute CA

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FTP down?
by John Clayton 15 Jun '12

15 Jun '12

Dear Sir or Madam, I have been attempting to upload a few datasets (>2Gb) for the past few days but I cannot seem to login to the server. This has been the case since the server crashed last week. Could you please restart the ftp server? Many thanks, John -- John R. Clayton, PhD Université de Strasbourg Anopheles Group, CNRS UPR-9022 "Réponse Immunitaire et Développement chez les Insectes" Institut de Biologie Moléculaire et Cellulaire (IBMC) 15, rue René Descartes F-67084 CEDEX Strasbourg France Tel: +33 3.88.41.70.96 Fax: +33 3.88.60.69.22 Email: j.clayton(a)ibmc-cnrs.unistra.fr http://www-ibmc.u-strasbg.fr/ridi/index.php?cont_id=9&lang=en

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GMOD Summer School now accepting applications
by Scott Cain 15 Jun '12

15 Jun '12

Applications are now being accepted for the 2012 GMOD Summer School course, a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD Components. The course will be held August 25-29 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. https://docs.google.com/a/scottcain.net/spreadsheet/embeddedform?formkey=dG… These components will be covered at the school: Apollo or WebApollo - genome annotation editor Chado - biological database schema Galaxy - workflow system GBrowse - genome viewer GBrowse_syn - synteny viewer GFF3 - genome annotation file format and tools InterMine - biological data mining system JBrowse - next generation genome browser MAKER - genome annotation pipeline Tripal - web front end to Chado databases The deadline for applying is the end of July 9, 2012. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2011 school had over 70 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $300 (only $60 per day). There will be a limited number of scholarships available. Thanks, Scott Cain -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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Galaxy in AWS AMI
by Lilach Friedman 14 Jun '12

14 Jun '12

Hi, Can somebody please help me? I'm trying for hours to connect to Galaxy on Amazon EC2. I did everything according the instructions, but did not succeed. The "Access Galaxy" button in the instance remains grey out. I copied the screen print and the log to the attached file. Can anyone help me please? and another questions: I want to use it to analyze MiSeq results (to align to the human genome). 100 Gb EBS and a large machine are enough? too much? Many thanks, Lilach.

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upload problem
by sujata dhar 14 Jun '12

14 Jun '12

Hello, I am trying to upload 27.2 GB fastq file in Galaxy through FTP, but it throws an error: netout: Connection reset by peer 421 Service not available,remote server has closed connection. Please help. Thank you, Sujata

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Page edition bug
by Felix Homa 14 Jun '12

14 Jun '12

Hi Galaxy team, I have two instances of galaxy on the same host, and have enabled page edition (I set enable_pages = True on universe_wsgi.ini file). I have set the parameter "cookie_path" different for each instance. I'm disconnected from galaxy when I try to edit a page content. But when I comment out the "cookie_path" for one instance it works for this instance. Did I miss something when configuring my instance ? Can someone give me some help ? I've tried to have a look at in the code but I'm not familiar with python. Thank you all, Felix Homa.

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Galaxy Reference Genome
by Kristen Roop 14 Jun '12

14 Jun '12

Hello, Galaxy Main 1.) I am having trouble adding annotations to my Tophat and Cufflinks tools. I used the Mus.Musculus 9MM reference using the *built in index. *For the Tophat mapping but no annotations were available in the output files. I then tried converting the the Ref Genome from the UCSC to a SAM file using Sam Tools. Tophat would not recognize this but Cufflinks did. The Cufflinks output file did not have the annotation either. Any thoughts on the proper way to add annotations? 2.) I am also trying to filter the single mapped reads from the multiple mapped reads that resulted from Tophat. After converting the output file from Tophat I used the filter tool in the Sam Tools choosing *0x100 map is not primary. *Afterwards I tried to run Cufflinks on the filtered output only to have it fail. My ultimate goal is to look at RNA seq gene expression. I know that I have to upload my files -> groom using FASTQ groomer -> download a reference sequence from UCSC -> convert the reference genome file to a usable format ->Run Tophat for mapping using the groomed file and the converted reference annotation -> Filter the single mapped reads -> Run cufflinks using the filtered single mapped reads from Tophat. >From here I will continue with some other statistical analysis but right now I need to get this basic pipeline to work. Thanks, Kristen Roop

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regarding Fusion transcript detection
by Amit Pande 13 Jun '12

13 Jun '12

Hi, Is there no tool in Galaxy which can detect chimera transcripts ??? warm regards, Amit

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