new cuffdiff with readgroup problem
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)
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:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson http://galaxyproject.org
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
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: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:
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
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: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:
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:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson http://galaxyproject.org
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 From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, November 15, 2013 10:23 PM 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 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:jen@bx.psu.edu] Sent: Thursday, October 31, 2013 4:09 AM 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 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
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