How To Keep Original Sample Names In Galaxy Through Cufflinks Pipeline?

Question: How To Keep Original Sample Names In Galaxy Through Cufflinks Pipeline?

6.5 years ago by

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.

rna-seq cufflinks • 1.1k views

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modified 6.5 years ago by Bidwell, Christopher A. • 30 • written 6.5 years ago by Christopher M. Weber • 30

6.5 years ago by

Bidwell, Christopher A. • 30

Bidwell, Christopher A. • 30 wrote:

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 ________________________________________ 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. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

ADD COMMENT • link written 6.5 years ago by Bidwell, Christopher A. • 30

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