Colleagues,
My solution to file naming issues are to use workflows which allow you to rename output files. In a cuffdiff work flow with replicates one can also name treatment groups which be used in the output. One can also rename the cuffdiff output to be compatible with the names cummeRbund expects to build the database.
The Galaxy# prefix will be there but the names you choose will be there too sorenaming of files is greatly simplified.
Chris Bidwell Purdue University
________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Christopher M. Weber [webercm@uw.edu] Sent: Monday, May 28, 2012 2:14 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] How To Keep Original Sample Names in Galaxy through Cufflinks pipeline?
Hello,
Overall Problem: Given sample names are not carried through Cufflinks pipeline. Instead, they are referenced with a number and in final Cuffdiff output are referred to as Sample 1/Q1, Sample 2/Q2 etc., instead of given name which requires tedious re-labeling.
Is there a way to implement -L function in Galaxy so that sample names are carried through from Cufflinks to Cuffdiff?
Originally posted in Seqanswers: http://seqanswers.com/forums/showthread.php?t=20338, where commenter suggested using -L as a fix but I don't see this option in Galaxy.
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