Kun:LabNotes/CpgSeq/2008-5-23: Difference between revisions
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===Mock read generation=== | ===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. | |||
Perl Script: [[Media:mockReadsGenV1.txt]] | Perl Script: [[Media:mockReadsGenV1.txt]] | ||
*I generated mock reads at 50X coverage (3,414,819 reads). 98% were mapped back to the target sequences with SOAP with the following parameters: | |||
-v 5 -e 10000 -c 0 -f 8 -r 0 -s 9 | -v 5 -e 10000 -c 0 -f 8 -r 0 -s 9 | ||
*To find out whether the 2% unmappable reads were due to multiple mapping positions or too many C:T mismatches, I generated another set of mock reads from completely methylated sequences (so that there is no C:T mismatch). It turned out that 100% reads were successfully mapped to the targets, which means the mapping strategy is bias towards methylated sequence. | |||
*I generated a third set of mock reads from completely unmethylated sequences, and performed the mapping with the same parameters. Only 85% reads were mappable. | |||
*I think the best mapping strategy is to map the reads to the completely methylated targets, and to the completely unmethylated targets, then take the union of the mapping results. |
Revision as of 20:04, 25 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.
Perl Script: Media:mockReadsGenV1.txt
- I generated mock reads at 50X coverage (3,414,819 reads). 98% were mapped back to the target sequences with SOAP with the following parameters:
-v 5 -e 10000 -c 0 -f 8 -r 0 -s 9
- To find out whether the 2% unmappable reads were due to multiple mapping positions or too many C:T mismatches, I generated another set of mock reads from completely methylated sequences (so that there is no C:T mismatch). It turned out that 100% reads were successfully mapped to the targets, which means the mapping strategy is bias towards methylated sequence.
- I generated a third set of mock reads from completely unmethylated sequences, and performed the mapping with the same parameters. Only 85% reads were mappable.
- I think the best mapping strategy is to map the reads to the completely methylated targets, and to the completely unmethylated targets, then take the union of the mapping results.