Difference: ProtocolsRunningBreseqOnTACC (4 vs. 5)

Revision 52016-06-21 - DanielDeatherage

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META TOPICPARENT name="ProtocolList"

Running breseq on TACC

Installing breseq on stampede for mac

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 See this page for information on generating .gd files.

Without using .gd files

Changed:
<
<
  1. Move to your scratch directory to make sure run can complete without space limits
>
>
  1. Move to your scratch directory to make sure run can complete without space limits.
 
    • cd $SCRATCH
Changed:
<
<
  1. Make a new project directory and change into that directory for better organization
>
>
  1. Make a new project directory and change into that directory for better organization.
 
    • mkdir New_Project
    • cd New_Project
Added:
>
>
    • mkdir Log_Files
  1. Copy all sequencing files and reference files to this New_Project directory.
    • For mac the scp command is useful for transferring files from your local computer to stampede (i.e. fastq files and reference files); For windows users, winscp is 1 possible solution.
 
  1. Generate a new "commands" file with 1 line for each sample you wish to analyze.
    • nano commands
  2. Each line should look like the following with possible additional information added into the __ space:
 
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