COMETgazer mehylation analysis software suite consists of 3 software:
- COMETgazer : bash script for methylome segmentation into COMETs based on OM values
Input : whole genome bisulfite sequencing methylation data that have been smoothed
Part of the bash script is blocks.cpp which is a C++ program assigning CpGs to COMETs
Example Input file : chr22.txt as an example of Chromosome 22 only. The software loops through all 22 chromosomes Example Output file : chr22_blocks_verified.txt example of COMET segmentation of Chromosome 22 only
- OORTcloud : bash script for counting COMET distributions according to methylation level
Input : this will be the output from COMETgazer e.g chr22_blocks_verified.txt. The software loops through all 22 chromosomes
Example Input file : chr22_blocks_verified.txt example of COMET segmentation of Chromosome 22 only. The software loops through all 22 chromosomes Example Output file : low.txt low methylation level COMET distribution genome wide medium.txt medium methylation level COMET distribution genome wide high.txt high methylation level COMET distribution genome wide
- COMETvintage : template R script for DMC analysis using edgeR
Example Input file : low.txt low methylation level COMET distribution genome wide for one methylome medium.txt medium methylation level COMET distribution genome wide for one methylome high.txt high methylation level COMET distribution genome wide for one methylome Example Output file : text file with the coordinates of DMCs