Kun:LabNotes/CpgSeq/2008-5-23

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Informatics

Read mapping

Should generate three files:

  1. Haplotype file: xxx.methylHap.txt
    1. One molecule per line;
    2. target_id, offset1, methylotype1, offset2, methylotype2...
  2. Methylation level file, average methylation level per site: xxx.methylFreq.txt
  3. Methylation LD statistics file, all LD statistics: xxx.methylLD.txt

Mock read generation

  1. 50% methylation at every CpG site;
  2. No correlation between adjacent CpG;
  3. Read position is evenly distributed;
  4. Can generate both single reads and pair-end reads;
  5. Incorporate an error model for sequencing;
  6. Should generate one raw read file and one methylHap file.