Re: [galaxy-user] new cuffdiff with readgroup problem

Fri, 15 Nov 2013 13:25:11 -0800 

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:[email protected]]
*Sent:* Thursday, October 31, 2013 4:09 AM
*To:* Johanna Sandgren
*Cc:* [email protected]; 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


___________________________________________________________
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