Calculation method for base methylation degree and program

A calculation method for a base methylation degree, comprising at least one selected from the group consisting of:

• (1) a method of calculating a base methylation degree at a target site on DNA having a co-methylation site, the method comprising:
• acquiring sequence analysis data obtained by subjecting DNA having at least one co-methylation site to a sequence analysis using a sequencer;
• correcting a base of the co-methylation site in a read based on quality information included in the sequence analysis data;
• and
• calculating a base methylation degree at the target site from corrected reads;
• (2) a method of calculating a base methylation degree at a target site on DNA having a co-methylation site, the method comprising:
• acquiring sequence analysis data obtained by subjecting DNA having at least one co-methylation site to a sequence analysis using a sequencer;
• correcting a read based on quality information included in the sequence analysis data and excluding a read in which a base does not coincide between the co-methylation sites;
• and
• calculating a base methylation degree at the target site from remaining reads;
• (3) a method of calculating a base methylation degree at a target site on DNA, the method comprising:
• acquiring sequence analysis data obtained by subjecting DNA to a sequence analysis according to a paired-end method using a next generation sequencer;
• correcting a paired-end read based on quality information included in the sequence analysis data;
• and
• calculating a base methylation degree at the target site from corrected reads;
• (4) a method of calculating a base methylation degree at a target site on DNA, the method comprising:
• acquiring sequence analysis data obtained by subjecting DNA to a sequence analysis according to a paired-end method using a next generation sequencer;
• correcting a read based on quality information included in the sequence analysis data and excluding a paired-end read in which a base at the target site does not coincide between the paired-end reads;
• and
• calculating a base methylation degree at the target site from remaining reads;
• (5) a method of calculating a base methylation degree at a target site on DNA, the method comprising:
• acquiring sequence analysis data obtained by subjecting DNA to which a molecular barcode is attached to a sequence analysis using a sequencer;
• correcting a read based on quality information included in the sequence analysis data;
• classifying corrected reads into a group of reads having the same molecular barcode;
• determining a base that most frequently appears at the target site on each of the read groups;
• and
• calculating a base methylation degree at the target site from a set of the bases that most frequently appear;
• (6) a method of calculating a base methylation degree at a target site on DNA, the method comprising:
• acquiring sequence analysis data obtained by subjecting DNA to which a molecular barcode is attached to a sequence analysis using a sequencer;
• correcting a read based on quality information included in the sequence analysis data;
• classifying corrected reads into a group of reads having the same molecular barcode, excluding a read having no identity in a sequence of a region including the target site in each of the read groups, and obtaining a read group having the same molecular barcode and the same sequence of the region including the target site;
• determining a base at the target site in each of the read groups having the same molecular barcode and the same sequence of the region including the target site;
• and
• calculating a base methylation degree at the target site from a set of the determined bases;
• (7) a method of calculating a base methylation degree at a target site on DNA, the method comprising:
• acquiring a plurality of sequence analysis data obtained by subjecting DNA to a plurality of sequence analyses using a sequencer;
• correcting a read based on quality information included in the sequence analysis data, for each of the sequence analysis data from an individual sequence analysis, and calculating a base methylation degree at the target site from corrected reads;
• and
• calculating a representative value from sets of the methylation degrees in all the sequence analyses and adopting the representative value as a base methylation degree at the target site;
• and
• (8) a method of calculating a base methylation degree at a target site on DNA, the method comprising:
• acquiring a plurality of sequence analysis data obtained by subjecting DNA to a plurality of sequence analyses using a sequencer;
• correcting a read based on quality information included in the sequence analysis data, for each of the sequence analysis data from an individual sequence analysis, and calculating a base methylation degree at the target site from corrected reads;
• and
• calculating a representative value from sets of the methylation degrees in all the sequence analyses and adopting the representative value as a base methylation degree at the target site,
• wherein in a case where the sets of the methylation degrees in all the sequence analyses vary from each other or include a specifically large or small methylation degree, or in a case where the sets of the methylation degrees in all the sequence analyses vary from each other and include a specifically large or small methylation degree, the representative value and the base methylation degree at the target site are calculated to be uncalculable.