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==The mapping strategy for CGI bisulfite sequencing reads== #Split raw reads into N subsets and process them separately; for each subset: ##Map reads to completely methylated target sequences, load the mapping results into memory; ##Map reads to completely unmethylated target sequences, load the mapping results and combine the two sets using the following rules: ###Accept the mapping if a read is mapped to the same target regardless the methylation status; ###Accept the one with fewer mismatches if a read is mapped to two different targets depending on the methylation status. ###Accept the mapping if a read is mapped to a target sequences in one methylation state. ##Report the mapping results. Perl Script: [[Media:mapBisSeqReadsV1.txt]] *For 3.4 million mock reads that contain 50% randomly methylation CpG sites, 98% were mapped with this strategy. I mapped the remaining 2% reads using Blast, and found that these reads have multiple mapping positions, which means they are not mappable anyway. *The work flow of data analysis would be: Raw reads [[Media:toMethylFreq.txt|=>]] methylFreq [[Media:methylFreq2BED.txt|=>]] UCSC Genome graph + ==> [[Media:MapBisReadsTargets.txt|Read mapper]] { => correlate with gene expression Targets => haplotype analysis [[Media:toCgiStat.txt|=>]] summary statistics of CGI
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