-- Fall10.AshrayU - 07 Dec 2009
Get GC Content in Jbrowse displayable WIG format from a FASTA file.
GCcontwig.pl converts oridnary single sequence FASTA files to WIG Files contating data on GC content per 5 nucleotides.
Note: Make sure the name in the fasta file is consistent with the name used in the fasta file prepare-refseqs.pl
Note: Make sure that the fasta file contains only the sequence you wish to generate wig data for.
Run from the terminal with the following command:
$ perl GCcontentwig.pl -calc yourfasta.FASTA -save output.wig
Add the track to jbrowse from terminal:
/www/jbrowse$ sudo bin/wig-to-json.pl --wig output.wig --key "GC Content" --fgcolor: "0,100,0"
Then continue to run the generate names script and load your jbrowse in your browser.
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