Re: [galaxy-user] replicates in cuffdiff output
Read group info isn't included in the Cuffdiff output right now. I've created a Trello card to fix this oversight: https://trello.com/c/FdUYdbIn Best, J. On Feb 18, 2013, at 12:32 PM, Johanna Sandgren wrote: > Hi, > > I am running cufflinks and cuffdiff using Galaxy. I am however wondering if > it is not supposed to be output files from cuffdiff regarding each replicate. > Anyone know why those (read.group-files) are not there, or when they will be > if it is because of the version used in Galaxy. I find it very valuable to > have those to be able to see intra/inter-group features in downstream > analysis. > > 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) > > ___ > 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/ ___ 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/
Re: [galaxy-user] Replicates
Hello Medhi, Sorry for the slow reply. It's not clear from your question, but let's assume that you have 3 lanes of RNA-seq data for each of your samples. In this case, here's a reasonable approach for analyzing this data: (1) Run Tophat + Cufflinks on each lane of data; (2) Use Cuffcompare on *all* transcripts produced by Cufflinks for all data; (3) Run Cuffdiff using (a) the combined transcripts produced by Cuffcompare and (b) segmenting the mapped reads produced by Tophat into groups based on the sample that they came from. Let us know if you have more questions. Thanks, J. On Feb 1, 2011, at 8:54 AM, Motallebipour, Mehdi wrote: > Hi, > > I am trying to analyze some RNA-seq data using the Galaxy. The reads for each > sample comes from 3 lanes, so I need to integrate these three lane reads to > be able to make a comparison between my samples. How do I 'put together' > these three read-files? Is there any tools available in Galaxy for that, > which I have missed? Unfortunately I do not have any programming skills. > > Many thanks, > Mehdi M > > Mehdi Motallebipour, PhD > Mammalian Neurogenesis > MRC Clinical Sciences Centre > Imperial College London > Hammersmith Hospital Campus > Du Cane Road > London > W12 0NN > United Kingdom > Tel: +44-20-8383 8285 > > > ___ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/
