Question: Cufflinks Output For Cummerbund
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Mike Shamblott • 20 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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modified 5.8 years ago
by
Jeremy Goecks • 2.2k
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written
5.8 years ago by
Mike Shamblott • 20
