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; 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)

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-- 
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