Cummerbund is available in the Galaxy toolshed for use in local or cloud
Galaxies:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
We haven't put it on our public server yet because there are testing and
compatibility challenges that need to be addressed.
Best,
J.
On Feb 11, 2013, at 7:49 PM, Mike Shamblott wrote:
> 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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