Re: [galaxy-user] Cuffdiff question
Dont use the - b parameter Sent from my iPhone; please excuse any brevity or typos! On Nov 15, 2013, at 2:51 PM, clare Hardman chard...@mrc-lmb.cam.ac.uk wrote: Hi Noa, Yes I did use Cufflinks so this sounds just like my problem. So how have you dealt with the problem? Best wishes, Clare On 14 Nov 2013, at 18:17, Noa Sher wrote: Hi Clare We just ran into a similar issue about a week ago and were debugging with the authors of cuffdiff Apparently there are issues with the -b parameter - were you using this in cufflinks? If yes - this may be the cause - we switched the order of the replicates and the values changed; as did PCA's of the samples, etc They are working on this issue for an upcoming version of cufflinks. I am interested in knowing whether this was indeed your problem or were you using a pipeline that does not include cufflinks? Good luck, Noa On 14/11/2013 13:13, clare Hardman wrote: Hello, Could you please advise me on this probably naive question. When I compare sample A and sample B by Ciffdiff and then separately compare Sample A to Sample C by Cuffdiff too, should the FMPK value be the same for A in both tests? At the moment mine does not seem to be! Best wishes Clare ___ 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/ ___ 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/
Re: [galaxy-user] Cuffdiff question
Hi Noa, Yes I did use Cufflinks so this sounds just like my problem. So how have you dealt with the problem? Best wishes, Clare On 14 Nov 2013, at 18:17, Noa Sher wrote: Hi Clare We just ran into a similar issue about a week ago and were debugging with the authors of cuffdiff Apparently there are issues with the -b parameter - were you using this in cufflinks? If yes - this may be the cause - we switched the order of the replicates and the values changed; as did PCA's of the samples, etc They are working on this issue for an upcoming version of cufflinks. I am interested in knowing whether this was indeed your problem or were you using a pipeline that does not include cufflinks? Good luck, Noa On 14/11/2013 13:13, clare Hardman wrote: Hello, Could you please advise me on this probably naive question. When I compare sample A and sample B by Ciffdiff and then separately compare Sample A to Sample C by Cuffdiff too, should the FMPK value be the same for A in both tests? At the moment mine does not seem to be! Best wishes Clare ___ 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/ ___ 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] how to add openstack in biocloudcentral ?
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 ___ 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] FW: Tophat/Cuff parameters
Hi Jen, Thanks again. Just to make it clear: if all the options are not present on galaxy but only some of them, does this mean that the absent ones have been set by galaxy dev? are these to be considered best settings not worth changing? I would like to learn a bit more and play with all options but if some of them wont affect the final reaults then is not worth changing them. Thanks, Irene From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: 14 November 2013 21:43 To: galaxy-user Cc: Irene Bassano Subject: Tophat/Cuff parameters 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-...@bx.psu.edumailto:galaxy-...@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-u...@bx.psu.edumailto:galaxy-u...@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 ___ 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/
Re: [galaxy-user] how to add openstack in biocloudcentral ?
Hi All, any update on this ? Zeeshan On Fri, Nov 15, 2013 at 2:24 PM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: 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 -- 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 ___ 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/
Re: [galaxy-user] FW: Tophat/Cuff parameters
Hello - Most of these are at defaults. The source code is the best place to find any that are hard-coded (if included, most likely done to manage resources). Again, any of of this could be modified if you have programming resource. The repository is owned by the devteam and in the Tool Shed, search with cuff here: http://usegalaxy.org/toolshed Best, Jen Galaxy team On 11/15/13 2:59 AM, Irene Bassano wrote: Hi Jen, Thanks again. Just to make it clear: if all the options are not present on galaxy but only some of them, does this mean that the absent ones have been set by galaxy dev? are these to be considered best settings not worth changing? I would like to learn a bit more and play with all options but if some of them wont affect the final reaults then is not worth changing them. Thanks, Irene *From:*Jennifer Jackson [mailto:j...@bx.psu.edu] *Sent:* 14 November 2013 21:43 *To:* galaxy-user *Cc:* Irene Bassano *Subject:* Tophat/Cuff parameters 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-...@bx.psu.edu mailto:galaxy-...@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-u...@bx.psu.edu mailto:galaxy-u...@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 ___ 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 ___ 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/
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 On 11/14/13 2:05 PM, Jennifer Jackson wrote: 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 On 11/12/13 12:26 AM, Johanna Sandgren wrote: 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:j...@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 -- 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 ___ 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/
