New Cuffdiff With Readgroup Problem

Question: New Cuffdiff With Readgroup Problem

5.1 years ago by

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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modified 5.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.1 years ago by Johanna Sandgren • 70

5.1 years ago by

Jennifer Hillman Jackson ♦ 25k

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Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.1 years ago by Jennifer Hillman Jackson ♦ 25k

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 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 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

ADD REPLY • link written 5.0 years ago by Johanna Sandgren • 70

Hi Johanna, Adding in the read_groups and other select output files is a planned enhancement for a future date. The Trello ticket to follow progress is here: https://trello.com/c/lIdpOZ88 related to : https://trello.com/c/U7nceKdj Good question! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Johanna, Update: I had this incorrect, the option to include "Read Group" files in the output is now available and near the bottom on the Cuffdiff tool form input option. Count tracking files are still in the list of open to-do items. Big thanks to Jeremy for the update! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I know read_group_tracking files are included now as I say in my e-mail below (before 11 output files now 15 from your cuffdiff) but the question was if also the count_tracking and/or read_group.info files are needed for plotting replicate data in CummeRbund, since I do not succeed with the current output. So now there is no difference what you can do (at least in CummeRbund) with the output compared to when it was 11 output files...? Even though you can choose "include Read Group Dataset" as I do. Thanks, Johanna To: Johanna Sandgren Cc: galaxy-user@lists.bx.psu.edu; Jeremy Goecks Subject: Re: [galaxy-user] new cuffdiff with readgroup problem Hi Johanna, Update: I had this incorrect, the option to include "Read Group" files in the output is now available and near the bottom on the Cuffdiff tool form input option. Count tracking files are still in the list of open to-do items. Big thanks to Jeremy for the update! Jen Galaxy team Hi Johanna, Adding in the read_groups and other select output files is a planned enhancement for a future date. The Trello ticket to follow progress is here: https://trello.com/c/lIdpOZ88 related to : https://trello.com/c/U7nceKdj Good question! Jen Galaxy team 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 To: Johanna Sandgren Cc: galaxy-user@lists.bx.psu.edu<mailto: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 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 -- Jennifer Hillman-Jackson http://galaxyproject.org ___________________________________________________________ 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

ADD REPLY • link written 5.0 years ago by Johanna Sandgren • 70

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