Question: Cufflinks Output For Cummerbund
gravatar for Mike Shamblott
5.8 years ago by
Mike Shamblott20 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
rna-seq cufflinks • 1.4k views
ADD COMMENTlink modified 5.8 years ago by Jeremy Goecks2.2k • written 5.8 years ago by Mike Shamblott20
gravatar for Jeremy Goecks
5.8 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Cummerbund is available in the Galaxy toolshed for use in local or cloud Galaxies: We haven't put it on our public server yet because there are testing and compatibility challenges that need to be addressed. Best, J.
ADD COMMENTlink written 5.8 years ago by Jeremy Goecks2.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour