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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