Kun:LabNotes/CpgSeq/2008-5-23: Difference between revisions
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(New page: ==Informatics== ===Read mapping=== Should generate three files: #Haplotype file: xxx.methylHap.txt *One molecule per line; *target_id, offset1, methylotype1, offset2, methylotype2... #Meth...) |
m (→Read mapping) |
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Should generate three files: | Should generate three files: | ||
#Haplotype file: xxx.methylHap.txt | #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 level file, average methylation level per site: xxx.methylFreq.txt | ||
#Methylation LD statistics file, all LD statistics: xxx.methylLD.txt | #Methylation LD statistics file, all LD statistics: xxx.methylLD.txt | ||
===Mock read generation=== | ===Mock read generation=== | ||
#50% methylation at every CpG site; | #50% methylation at every CpG site; |
Revision as of 21:59, 23 May 2008
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.