File format

File format#

CpG start indexed format#

The CpG Start Indexed (CGS) format comprises two mandatory columns along with several informational columns:

  • Sequence name [chrom]: chromosome number or sequence names

  • CpG index [cpg_index]: This column lists the sequential positions of CpG sites., 1-based, end-inclusive position of the CpG index

  • Informational columns [optional]: column 3 to column n,

chr1	1	c3	c4
chr1	2	c3	c4
chr1	3	c3	c4
chr1	4	c3	c4

The file header is prefixed with a # symbol. The entire file is compressed using bgzip and indexed with tabix. Below is an example:

bgzip demo.cgs
tabix -C -s 1 -b 2 -e 2 demo.cgs.gz

PAT format#

PAT is a CGS-based format, containing 4 columns:

  • Sequence name

  • CpG index

  • Methylation motif: This column denotes the methylation status of the CpG site

    • ‘C’: methylated CpGs

    • ‘T’: unmethylated CpGs

    • ‘.’: unknown methylation status

  • Motif count: This column records the frequency of each motif described in column 3

chr1    755     CCCTCCCCTCTTCCT 1
chr1    755     TTTT    2
chr1    756     CCCCCTC 1
chr1    756     CCCCCT....CCCC  10
chr1    758     CCCCCCCCCCCC    4
chr1    758     CCTTCCCTCCC     1

MV format#

MV (methylation vector) format is a CGS-based format

MVC format#

MVC (methylation vector cluster) format is a CGS-based format

MVM format#

MVM (methylation vector matrix) format is a CGS-based format

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