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===Increase the stringency for definine informative bins.=== *When manually inspecting the mld_blocks for the promoter regions of a few cancer genes, such as SEPT9 and SDC2, I found that mld_blocks can be quite large, containing ~100 CpG sites. Having such large blocks makes it difficult to compare haplotypes, because different haplotypes in a block might not overlap at all. *I tested several cutoff values for r2, including 0.3, 0.5 and 0.7, on chr4 and manually inspect the partitioning of the SDC2 promoter. I found that 0.5 is probably a more appropriate cutoff. *Therefore, I used r2>=0.5 to repeat the partitioning of mld_blocks ([[Media:Batch_WGBS_RRBS_CapSeq_mld_block_partitioning_stringent.txt| Batch processing script]]). I ended up having close to 300k blocks covering ~1% of the genome. Comparing with the blocks with r2>=0.1, the average block size is similar, and the total number of blocks was reduced to ~30%. {| {{table}} | align="center" style="background:#f0f0f0;"|'''Chromosome''' | align="center" style="background:#f0f0f0;"|'''Total_block_size(bp)''' | align="center" style="background:#f0f0f0;"|'''Average_block_size(bp)''' | align="center" style="background:#f0f0f0;"|'''Number_of_blocks''' |- | chr1||2,331,103||87||26,650 |- | chr2||1,889,469||85||22,164 |- | chr3||1,442,988||90||15,995 |- | chr4||1,095,979||84||12,973 |- | chr5||1,265,930||87||14,607 |- | chr6||1,470,508||91||16,232 |- | chr7||1,307,725||81||16,050 |- | chr8||1,107,303||85||13,085 |- | chr9||1,083,570||85||12,723 |- | chr10||1,248,282||84||14,900 |- | chr11||1,299,293||87||14,851 |- | chr12||1,263,831||89||14,183 |- | chr13||623,564||83||7,533 |- | chr14||851,644||87||9,754 |- | chr15||848,814||86||9,893 |- | chr16||1,070,257||83||12,836 |- | chr17||1,350,521||83||16,342 |- | chr18||538,930||80||6,719 |- | chr19||1,319,181||85||15,527 |- | chr20||708,615||84||8,481 |- | chr21||326,002||77||4,238 |- | chr22||575,079||81||7,123 |- | Total||25,018,588||||292,859 |- | |}
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