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Revision as of 12:31, 5 April 2013
, 12:31, 5 April 2013no edit summary
Note this path as you will need to set the variable '''REF_DIR''' in the configuration file or options
Note this path as you will need to set the variable '''REF_DIR''' in the configuration file or options
'''gen_biopipeline.pl''' and '''umake.pl'''.
'''gen_biopipeline.pl''' and '''umake.pl'''.
= Using Your own Reference Files =
== Human Reference ==
=== Generating GCContent File ===
To generate the GC content file, run qplot:
GOTCLOUD_DIR/bin/qplot --reference reference.fa --winsize windowSize --create_gc reference.gc
* Replace reference.fa with the name of your human reference fasta file.
* Replace windowSize with your desired window size, or leave out --winsize to use the default.
http://genome.sph.umich.edu/wiki/QPLOT#Input_files
