NAME

trinucleotide_genome.pl

SYNOPSIS

trinucleotide_genome.pl [options] [file ...]

        Options:
        --help                          brief help message
        --man                           full documentation
        --genome                        Genome FASTA in which to parse trinucleotide information (default = "None")
        --trinucleotide_dir location to generate the trinucleotide information files (Required)
        --cb_bed_dir            location to the bed files where callable bases information can be found (default = "None")
        --filtered_dir          location to generate the filtered trinucleotide files (default = "None")
        --chromosome            chromosome or name of fasta sequence specified to act upon only (default = "None")
        --zip_files             whether to zip the trinucleotide files generated (default: Y)
        --only_zip                      whether to only zip files in the directory and run nothing else (default: N)

OPTIONS

--help

Print a brief help message and exit.

--man

Print the manual page.

--genome

Genome FASTA in which to parse trinucleotide information (default = "None").

--trinucleotide_dir

Location to generate the trinucleotide information files.

--cb_bed_dir

Location to the bed files where callable bases information can be found (default = "None").

--filtered_dir

Location to generate the filtered trinucleotide files (default = "None").

--chromosome

Chromosome or name of fasta sequence specified to act upon only (default = "None").

--zip_files

Whether to zip the trinucleotide files generated (default: Y).

--only_zip

Whether to only zip files in the directory and run nothing else (default: N).

DESCRIPTION

trinucleotide_genome.pl Reads the reference genome by 3 nucleotide window and store the information

 - read the reference genome by 3 nucleotides windows
 - create hash table of genome locations by trinucleotide context
 - makes a directory for each of the sequences provided in the genome fasta, or for the chromosome specified
 - write the chromosome and middle nucleotide location to trinucleotide file
 - uses callable bases bed file to filter trinucleotides so only callable ones are hashed
 - zips files with gzip through system call

EXAMPLE

Typical usage:

        trinucleotide_genome.pl --genome /path/to/your/sample.fasta --trinucleotide_directory /directory/to/save/files

        trinucleotide_genome.pl --genome /path/to/your/sample.fasta --trinucleotide_directory /directory/to/save/files --chromosome ${chrom} --cb_bed_dir /directory/to/your/beds

AUTHOR

Lydia Liu

Boutros Lab The Ontario Institute for Cancer Research

ACKNOWLEDGEMENTS

Paul Boutros, PhD, PI -- Boutros Lab

Srinivasan Sivanandan -- Boutros Lab

SEE ALSO

generate_signature.pl --man

BAMsurgeon.pl --man