Kun:LabNotes/CpgSeq/2008-5-23
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Informatics
Read mapping
Should generate three files:
- Haplotype file: xxx.methylHap.txt
- One molecule per line;
- target_id, offset1, methylotype1, offset2, methylotype2...
- Methylation level file, average methylation level per site: xxx.methylFreq.txt
- Methylation LD statistics file, all LD statistics: xxx.methylLD.txt
Mock read generation
- 50% methylation at every CpG site;
- No correlation between adjacent CpG;
- Read position is evenly distributed;
- Can generate both single reads and pair-end reads;
- Incorporate an error model for sequencing;
- Should generate one raw read file and one methylHap file.