To use hg16, hg17, or hg18, set gene_file=folder containing the gene information files. By default, hg19 is used and is installed with CRaVe. The files are named chr_xx.txt.gz.
Each file contains the columns:
Column 1: gene name
Column 2: gene start position
Column 3: gene end position
Column 4: codon start position
Column 5: codon end position
Column 6: number of exon start and end positions
Column 7: comma separated list of exon starting positions
Column 8: comma separated list of exon ending positions
The files must be tab-delimited and sorted by ascending gene start position. Row 1 has the total number of rows in the file minus 1. Row 2 are the column names. Use the command "tar –xzvf hg18.tar.gz" to un-pack the files.