Hello, Thanks for your answer. I can see that compared to the output from cuffdiff according to their manual (http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff) there are still files missing from galaxy's output. Like the count tracking files and read_groups, info. So these are vital for replicate plotting in CummeRbund then? When will you also include them in your output? Regards, Johanna From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Thursday, October 31, 2013 4:09 AM To: Johanna Sandgren Cc: galaxy-user@lists.bx.psu.edu; Jeremy Goecks Subject: Re: [galaxy-user] new cuffdiff with readgroup problem Hello Johanna, Last time I checked, this specific functionality was not fully implemented yet. I do not believe that a firm timeline has been set yet for completion. Jeremy can comment if I have this incorrect, but I wanted to get back to you so that you were not wondering! Take care, Jen Galaxy team On 10/21/13 8:54 AM, Johanna Sandgren wrote: 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) ___________________________________________________________ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org