[galaxy-user] Cuffdif output NOTEST
Dear all, I have Illumina RNAseq data and want to look for differences in gene expression between male and female rats and transgenic vs. wildtype; for each condition I have triplicates. I mapped with TopHat for Illumina, using the reference genome rn5 and default settings. I did Cuffdiff afterwards and used the GTF-file Rattus norvegicus.Rnor_5.0.72.gtf as transcript. As result I got no significant changes in expression and it always says NO TEST (or sometimes LOW DATA). I found that lowering or raising the -c option might control the cuffdiff behavior, but I do not know what it is and how to control it. Can you explain me how to do it? And would you advise me to use another transcript for Cuffdiff? And when yes, where can I get it? Lots of questions. Thanks in advance for your answer. Best, Meike ___ 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/
[galaxy-user] Update from server failed several times
Hello, I deleted some files, because I reached 100% of the data volume I could use; my actual volume is 76 GB. I'm waiting now for an update from the server, that I reduced the data volume and can continue with my analysis. But I got a red note on the history for several times, that the update failed and that I should contact you, when it does so. What could I do now, to get an update from the server? Thanks in advance! Best, Meike ___ 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/
[galaxy-user] Help: Mapping with Bowtie does not start
Hello, I am trying to map sequences with Bowtie for Illumina. I have been waiting for a whole day now but it still says Job is waiting to run. Are the jobs stuck in a queue or is there any other problem? Thanks a lot in advance! Meike ___ 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/
