[galaxy-user] Cuffdiff-cummerbund with biological replicates problem

[Mike Shamblott]

I'm trying to run Cuffdiff on a set of 10 human samples with biological 
replication then download the results for further analyses in 
Cummerbund(v2.1.1).  It seems like a standard workflow but I cannot get 
cummerbund to acknowledge replicates.  I download and rename the 11 cuffdiff 
output files to the names expected by cummerbund.  Cummerbund builds a CuffSet 
with no warnings and most analyses work as expected.  The problem comes any 
time I try to see the results of replication.  For example, in cummerbund, 
replicates() returns an empty set and any type of plot returns an error when 
replicates=T is included as an argument.

There is no evidence of replication data in any of the 11 cuffdiff output 
files.  The data is presented with the group name only.  From this, I conclude 
that the problem is with cuffdiff, since there is no replicate data for 
cummerbund to build into its db.  I see that there are several read group files 
that are produced by cuffdiff but cannot be downloaded in Galaxy.  Is this the 
problem, and if so, how can Galaxy be used to generate data with (essential) 
replication?  Are the p  and  q significance values reported in the output 
files a result of replicate analysis?  


I have tried to ask this question in several different forums without success.  
The responses I've gotten suggest its a Galaxy issue rather than either 
cuffdiff or cummerbund.   I'm hoping someone here can help answer my questions.

Hopeful,

Mike___
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[galaxy-user] cufflinks output for cummeRbund

[Mike Shamblott]

I have been using cufflinks on Galaxy Main.  I have downloaded the files 
generated but they do not correspond to the file names expected by cummeRbund.  

For example:
cummeRbund expects 4 tracking files (e.g isoforms.fpkm_tracking) , 4 .diff 
files (e.g isoform_exp.diff).  

Here is a trimmed version of the output I download, grouped by what Im guessing 
is the tracking, diff and usage files:


TRACKING
...Galaxy109_transcript_FPKM_tracking.tabular
...Galaxy107_gene_FPKM_tracking.tabular
...Galaxy105_TSS_groups_FPKM_tracking.tabular
...Galaxy103_CDS_FPKM_tracking.tabular


.DIFF

...Galaxy108_transcript_differential_expression_testing.tabular
...Galaxy106_gene_differential_expression_testing.tabular

...Galaxy102_CDS_FPKM_differential_expression_testing.tabular

USAGE
...Galaxy99_splicing_differential_expression_testing.tabular

...Galaxy100_promoters_differential_expression_testing.tabular

...Galaxy101_CDS_overloading_differential_expression_testing.tabular



Given that cummeRbund is a common next step in the workflow, is there an option 
to save the output in the expected format, perhaps with a galaxy history number 
prepend?  I'm not sure which files are to be renamed and to what name and it 
seems that one file is missing.

If there were a cummeRbund implementation on Main it probably wouldn't matter 
as much but until that happens, I (and i'm guessing other newcomers) would 
appreciate the help!

Thanks,

mike___
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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