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

2013-11-12 Thread Johanna Sandgren 
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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[galaxy-user] Cuffdiff question

2013-11-12 Thread Jennifer Jackson 

Hello,

The transcript name when using RefSeq as a reference annotation is the 
NM_ type of identifier.


If you want to include a gene symbol, then the reference annotation 
should include the attribute gene_name. The iGenomes GTF files are an 
example of datasets that include this attribute.


http://wiki.galaxyproject.org/Support#Interpreting_scientific_results
See: /Example/?/*RNA-seq analysis*/*tools*
http://cufflinks.cbcb.umd.edu/faq.html#gtfs
http://cufflinks.cbcb.umd.edu/igenomes.html
http://cufflinks.cbcb.umd.edu/manual.html (search on page for 
gene_name to see where can be used/output)


Best,

Jen
Galaxy team

On 11/12/13 10:40 AM, Irene Bassano wrote:

Dear Jennifer,
I am about to start a new analysis and learning from my old mistakes would like 
to ask just one question:
I would like my Cufflinks and Cuffdiff results to give me the actual gene name or 
transcript name rather than NM_.. like I had last time i run the job.

At which stage and which option do I have ti use to get the proper names?

Thanks a lot!

Irene


--
Jennifer Hillman-Jackson
http://galaxyproject.org

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Jennifer Hillman-Jackson
http://galaxyproject.org

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