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Revision as of 01:10, 18 June 2014
, 01:10, 18 June 2014→Copy to Text File
You now have a tab delimited align.2x.index file (a little simpler than yesterday).
You now have a tab delimited align.2x.index file (a little simpler than yesterday).
== Create your GotCloud Configuration File ==
Now that you have your FASTQ info file created, we need to setup the configuration.
'''If you updated your gotcloud.2x.conf file yesterday, you still need to do this step'''
* We updated a few settings to match 1000g
*# Updated the version of the genome reference
*# Updated to use BWA instead of BWA_MEM
*# Updated the version of BWA
You can copy from my directory to your personal directory:
cp /home/mktrost/seqshop/inputs/gotcloud.2x.conf ~/personal/.
You need to update the conf file to find your align.2x.index and ensure your output directory is setup.
nedit ~/personal/gotcloud.2x.conf &
(or use your favorite editor)
* Change the <code>IN_DIR</code> line, replacing <code>YOUR_USER_NAME</code> with your user name.
* Everything else is configured already.
[[File:Gc2xconf.png]]
You'll notice that this file is very similar to the one we have been using.
* Just a few modifications to run a new test on the whole genome
