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Revision as of 14:25, 5 July 2013
, 14:25, 5 July 2013→Generating GCContent File
See http://bio-bwa.sourceforge.net/bwa.shtml for more information about using "bwa index".
See http://bio-bwa.sourceforge.net/bwa.shtml for more information about using "bwa index".
=== Generating GCContent File ===
=== Generating GC Content File ===
The GC Content file is used by QPLOT. It is assumed to be at the same location as the reference file.
If the reference file is at path/ref.fa, the GC Content file is expected to be:path/ref.winsize100.gc
To generate the GC content file, run qplot:
To generate the GC content file, run qplot:
GOTCLOUD_DIR/bin/qplot --reference reference.fa --winsize windowSize --create_gc reference.gc
GOTCLOUD_DIR/bin/qplot --reference reference.fa --winsize windowSize
* Replace reference.fa with the name of your human reference fasta file.
* 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.
* Replace windowSize with your desired window size, or leave out --winsize to use the default (100).
http://genome.sph.umich.edu/wiki/QPLOT#Input_files
NOTE: You will get an error at the end of qplot that says:
<pre>
FATAL ERROR -
No SAM/BAM files provided, stopped!
</pre>
This error is due to using qplot to just generate a GC Content file and not also process a BAM file.
But it was successful as long as you see (where reference is the name of your reference file):
<pre>
GC content file [ reference.winsize100.gc ] created.
</pre>
See http://genome.sph.umich.edu/wiki/QPLOT#Input_files for more information.
