swebb1/cpg_tools

cpg_tools

CpG.pl

Calculate CpG statistics over entire fasta record.

--infile: Input fasta file --outfile: Output file --nthresh: Include fasta records with this fraction of Ns or less (use a fraction of 1).

CpGwindow.pl

Split fasta record in to a window of defined size and calculate CpG statistics per window.

--infile: Input fasta file --outfile: Output file --window: Window length --step: Step size --nthresh: Include fasta records with this fraction of Ns or less (use a fraction of 1)

CpGseq.pl

Generate random sequences using parameters of length, GC content and CpG observed/expected ratio.

--out: Output file --length: Approxiamate length of output sequence --GC: GC% content of output sequence --CpG: CpG observed/expected ratio of output sequence