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== Check chromosome and coordinate of CpG and SNP derived from mapping by bisReadMapperSE19Triton and from Robert's ASM pipeline == * bisReadMapperSE19Triton mapping * 509557 GK0005-001.hg19.BED.txt sort GK0005-001.hg19.BED.txt > sorted_chrpos_GK0005-001.hg19.BED.txt 509557 sorted_chrpos_GK0005-001.hg19.BED.txt track name="GK0005-001_hg19" description="Methylation level" visibility=2 useScore=1 itemRgb="On" chr10 100017297 100017298 0.983 58 + 100017297 100017298 210,0,0 chr10 100017304 100017305 0.930 57 + 100017304 100017305 210,0,0 chr10 100017325 100017326 1.000 58 + 100017325 100017326 210,0,0 chr10 100017333 100017334 0.964 55 + 100017333 100017334 210,0,0 chr10 100029179 100029180 0.951 41 + 100029179 100029180 210,0,0 chr10 100029247 100029248 0.450 40 + 100029247 100029248 90,150,0 chr10 100029342 100029343 0.026 39 + 100029342 100029343 0,240,0 chr10 100029476 100029477 0.897 58 + 100029476 100029477 210,0,0 chr10 100029482 100029483 0.276 58 + 100029482 100029483 60,180,0 * Robert's pipeline 488563 CpGMethFreq.GK0005001.bed sort CpGMethFreq.GK0005001.bed > sorted_CpGMethFreq.GK0005001.bed 488563 sorted_CpGMethFreq.GK0005001.bed track name="GK0005001 CpG MF" description="GK0005001 CpG Methylation Frequency" visibility="dense" useScore=1 itemRgb="On" chr10 100017297 100017298 0.982 57 + 100017297 100017298 210,0,0 chr10 100017304 100017305 0.929 56 + 100017304 100017305 210,0,0 chr10 100017325 100017326 0.999 57 + 100017325 100017326 210,0,0 chr10 100017333 100017334 0.965 57 + 100017333 100017334 210,0,0 chr10 100029179 100029180 0.950 40 + 100029179 100029180 210,0,0 chr10 100029247 100029248 0.450 40 + 100029247 100029248 90,150,0 chr10 100029342 100029343 0.026 39 + 100029342 100029343 0,240,0 chr10 100029476 100029477 0.897 58 + 100029476 100029477 210,0,0 chr10 100029482 100029483 0.276 58 + 100029482 100029483 60,180,0 * The number of called CpG by Robert's pipeline was lower than bisReadMapperSE19Triton. This is possible that Robert's pipeline is more stringent than bisReadMapperSE19Triton, so the number of called CpG was lower. However the chromosome positions, CpG coordinates and methylation frequency were consistent.
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