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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