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)
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