allelic - Single-site ASM scoring

Synopsis

$ dnmtools allelic [OPTIONS] <input.epiread>

Description

The program allelicmeth calculates allele specific methylation scores for each CpG site. Input files should be the epiread files (.epiread suffix) produced using states. In the output file, each row represents a CpG pair made by any CpG and its previous CpG, the first three columns indicate the positions of the CpG site, the fourth column is the name including the number of reads covering the CpG pair, the fifth column is the score for ASM, and the last four columns record the number of reads of four different methylation combinations of the CpG pair: methylated methylated (mm), methylated unmethylated (mu), unmethylated methylated (um), or unmethylated unmethylated (uu). The following command will calculate allele specific methylation scores using the allelicmeth component of dnmtools:

$ dnmtools allelic -c /path/to/genome.fa -o output.allelic input.epiread

Options

 -o, -output

output file name (default: STDOUT)

 -c, -chrom

FASTA file or directory of chromosomes containing FASTA files [required]

 -v, -verbose

print more run info to STDERR while the program is running.