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Quantmap output issue (chemical names are truncated and cannot be differentiable from each other)
by Hsieh, Jui-Hua (NIH/NIEHS) [E] 20 Nov '13

20 Nov '13

Hi, I have submitted chemicals to the QuantMap. The chemicals are successfully prepared by the "QuantMap Prep" and run by "QuantMap server". However, in the output files (dendrogram as well as the cluster information), all of the chemical names are truncated. Thus, some chemicals with identical truncated names cannot be differentiated from each other. I wonder if CIDs or full chemical names can be reported as well. Thank you, Jui-Hua

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compute an expression on every row question
by Tobias Hohenauer 20 Nov '13

20 Nov '13

Hello, I am looking for the right way to do a computation using "text manipulation, compute an expression on every row". I have a table consisting of 20 columns and about 15.000 rows. Column 1 is my untreated or control and I would like to normalize every other column to this control by simple division. As a result I would like to obtain a table in which column 1 is set to a value of 1 for every row, and the corresponding values in the other columns resulting from column x / column 1. I tried something like c2/c1,c3/c1,c4/c1... on a small testfile but that results in all normalized values being put into one column in brackets rather than being put into individual columns. What would be the right parameters? I also thought about creating a workflow consisting of successive divisions of the columns but that feels rather complicated. Is there an easier way? Any help would be much appreciated! Best, Tobias -- Tobias Hohenauer, PhD GCNA, Disease Mechanism Research Core RIKEN Brain Science Institute 2-1 Hirosawa, Wako-shi 351-0198 Japan

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new cuffdiff with readgroup problem
by Johanna Sandgren 19 Nov '13

19 Nov '13

Hi, I have tested the new cuffdiff version in galaxy and was very eager to now also get the replicate data for each test. Have anyone tried that yet and succeeded with replicates in downstream R package CummeRbund? Even though I successfully build database with the now 15 output files (including read group tracking), no error message, I can not plot anything with replicates=T. Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near "from": syntax error) Anyone know the problem? Thanks, Johanna ...................................................................................................................................................... Johanna Sandgren, PhD Department of Oncology-Pathology CCK, Karolinska Institutet SE-171 76 Stockholm, Sweden +46-8-517 721 35 (office), +46-8- 321047(fax), +46-708 388476 (mobile)

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Mean inner distance
by Jennifer Jackson 18 Nov '13

18 Nov '13

Hi Vanessa, Mean inner distance can be thought of as being the estimated gap left between the two ends of the paired reads. This is from the manual (also at the bottom of the Tophat tool form): > -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments > selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter > is required for paired end runs. In short, take the insert size, subtract the length of both sequenced ends, and that is the "Mean inner distance". Best, Jen Galaxy team On 11/18/13 10:08 AM, Vanessa Lattimore wrote: > Hi Jen, > I was hoping you would be able to clarify something for me. What is the mean inner distance between mate pairs in the TopHat tool? I can't find a consensus online on what it is and everything I have found seems to be guesses. > My data was run on the HiSeq, and the average insert size was ~200 prior to all adaptors being removed. Do I go off this to determine the inner distance or is there a pipeline of tools I need to use to accurately determine it? > Your help would be greatly appreciated! > Many regards, > > Vanessa. -- Jennifer Hillman-Jackson http://galaxyproject.org

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bowtie2
by mark.rose＠syngenta.com 18 Nov '13

18 Nov '13

Hi All I'm trying to use bowtie2 in Galaxy but though I have uploaded a valid pair of fastq files, Galaxy seems to recognize only one of the and places it in both inputs for paired end reads without any other options in the drop down menus. Thanks for your help Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Blast on Galaxy?
by Jorge Braun 18 Nov '13

18 Nov '13

hello users, 😊 My name is J.Braun and I am a new user of galaxy... It is a great tool for biologists. I have some questions and I would appreciate you could help me. 1) can I make a blast in Galaxy? 2) If so, can I download blast in galaxy? 3) If so, can I set up blast in my galaxy for analysis with only a particular species? Thank you very much

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Tophat/Cuff parameters
by Jennifer Jackson 17 Nov '13

17 Nov '13

Hello, Yes, this is correct, not all parameters can be adjusted in the UI. Many can, especially with Tophat, but not all. The list of implemented parameters that will match the documentation is listed at the bottom of each of these tools. The UI form itself up top may have a slightly different human readable name, but most will include the parameter name "-r", etc. To see all of the parameters on the forms: 1. Tophat/2 - open "TopHat settings to use: Full parameter list" 2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full content This tool is in the Tool Shed (http://usegalaxy.org/toolshed) so if you had programming resource available, then these could certainly be modified. Development questions can go do the galaxy-dev(a)bx.psu.edu mailing list, but really the best place to start is in our wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax http://wiki.galaxyproject.org/Tool%20Shed It would be really helpful if you sent questions directly to the galaxy-user(a)bx.psu.edu mailing list going forward. Thanks, Jen Galaxy team On 11/14/13 1:08 PM, Irene Bassano wrote: > Hi Jen, > thanks a lot for your reply. > > I am trying to apply some changes to certain parameters in cufflinks. I have read them on the manual but on galaxy are not all listed. > is this because they have been chosen already by galaxy and set to certain values you guys believe are optimal? > I cannot find for example: > > Maximum genomic length allowed for a given bundle. > Minimum intron size allowed in genome. > Minimum average coverage required to attempt 3' trimming. > > and many others. > > I also wanted to access full parameters for Tophat and Cuffdiff... > > Any suggestion on how can I access them? > > Thanks, > Irene -- Jennifer Hillman-Jackson http://galaxyproject.org

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how to add openstack in biocloudcentral ?
by Zeeshan Ali Shah 15 Nov '13

15 Nov '13

Hi, I followed the guide from https://github.com/chapmanb/biocloudcentral and managed to run locally, But only see AWS in combo box, How to add private Openstack in it? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

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Cuffdiff question
by Jennifer Jackson 15 Nov '13

15 Nov '13

Hello, The transcript name when using RefSeq as a reference annotation is the "NM_" type of identifier. If you want to include a gene symbol, then the reference annotation should include the attribute "gene_name". The iGenomes GTF files are an example of datasets that include this attribute. http://wiki.galaxyproject.org/Support#Interpreting_scientific_results See: /Example/?/*RNA-seq analysis*/*tools* http://cufflinks.cbcb.umd.edu/faq.html#gtfs http://cufflinks.cbcb.umd.edu/igenomes.html http://cufflinks.cbcb.umd.edu/manual.html (search on page for "gene_name" to see where can be used/output) Best, Jen Galaxy team On 11/12/13 10:40 AM, Irene Bassano wrote: > Dear Jennifer, > I am about to start a new analysis and learning from my old mistakes would like to ask just one question: > I would like my Cufflinks and Cuffdiff results to give me the actual gene name or transcript name rather than "NM_......" like I had last time i run the job. > > At which stage and which option do I have ti use to get the proper names? > > Thanks a lot! > > Irene -- Jennifer Hillman-Jackson http://galaxyproject.org -- Jennifer Hillman-Jackson http://galaxyproject.org

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Setting a queue for torque submission
by Xian Su 14 Nov '13

14 Nov '13

Greetings I'm having a hard time getting job submission to work via torque. Posted below is the relevant part of my universe file and job_conf.xml. The main cause comes from our torque server requiring a queue to be requested. I can submit jobs just fine via job .sub files via command line using qsub -q M30 Running jobs via webgui results in the following: galaxy.jobs.runners.pbs WARNING 2013-11-14 13:54:23,722 (28) pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs ERROR 2013-11-14 13:54:25,724 (28) All attempts to submit job failed On the torque server's pbs logs, I see the corresponding 11/14/2013 13:54:23;0080;PBS_Server.66159;Req;req_reject;Reject reply code=15039(No default queue specified MSG=requested queue not found), aux=0, type=QueueJob, from xians(a)podmt1-100-62.novalocal In my universe_wsgi.ini, I'm currently using the settings: start_job_runners = pbs default_cluster_job_runner = pbs:///-q M30 -l nodes=1:ppn=12/ ^I mainly have no idea how to find the correct syntax for this pbs:/// But when I comment out default_cluster_job_runner and instead uncomment the line for the following job conf, I get the same error: <?xml version="1.0"?> <job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> </plugins> <handlers default="handlers"> <handler id="main" tags="handlers"/> </handlers> <destinations default="pbs"> <destination id="local" runner="local"/> <destination id="pbs" runner="pbs" tags="mycluster"> <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=12</param> <param id="-q">M30</param> </destination> </destinations> <tools> <tool id="main" handler="main" destination="pbs"/> </tools> <limits> </limits> </job_conf> Thank you in advance for any help. Regards, Xian

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