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* '''Link to calendar''': [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]] == 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. == Check the CpG coordination in ASM output file == * To check if the CpG coordinate from ASM analysis is on start or end position. ** CpG coordinates in methylFreqMatrix generated by the BED file mapped by bisReadMapperSE19Triton are on the end position awk '{print $1"\t"$2}' UCLA-4batches_methyl-noSNP_min76_minSTD0.1.txt | head -3 0chr_position GK0005-001 '''chr13:45885186''' 0.701 '''chr7:105318897''' 0.680 less GK0005-001.hg19.BED.txt chr13 45885185 '''45885186''' 0.701 144 + 45885185 45885186 150,90,0 chr7 105318896 '''105318897''' 0.680 25 + 105318896 105318897 150,90,0 * File's description: (9) MFASMAnalysisPValues.$expname.$asmtesttype.txt 1st field is the SNP coordinate, 2nd field is the SNP call, 3rd field is the strandedness of the SNP call (ss - single strand ds - double strand), 4th field is the strand of the SNP call, 5th field is the type of calculation (a number stands for the coordinate of a specific CpG. Stable and stable average are defined above). 6th field shows the difference in methylation frequency values between CpGs on SNP bases 1 and 2 7th field is the p-value associated with the observed allele specific differential methylation values. 8th and 9th are the number of C's and T's associated with SNP base1, respectively. Fields 10 and 11 are the number of C's and T's associated with SNP base2, respectively. '''MFASMAnalysisPValues.GK0005001.cpg.txt''' 3:173374 AG ss - '''173345''' -0.0262626262626262 0.783557175124665 36 8 38 7 '''CpGMethFreq.GK0005001.bed''' chr3 173344 '''173345''' 0.831 89 + 173344 173345 180,60,0 '''MFASMAnalysisPValues.GK0005001.cpg.txt''' 20:62405863 CG ss - '''62405854 ''' 0.153846153846154 0.402328024619046 22 4 9 4 '''CpGMethFreq.GK0005001.bed''' chr20 62405853 '''62405854''' 0.810 42 + 62405853 62405854 180,60,0 * This means that the CpG coordinates from ASM analysis are on the end position as the CpG in methylFreqMatrix as well == Check SNP == *In the SNP file from bisReadMapperSE19Triton mapping (1) chromosome name (2) position (3) reference base call (4) strand (Watson/Crick) (5) variant call (6) variant quality (7) total read depth (8,10,12..etc) depth of sequenced base (9,11,13..etc) base sequenced * SNPs before filtered chr12 '''25537917''' A C A 157 44 A 44 chr16 '''84539303''' C C K 49 21 T 6 G 15 chr2 '''44588941''' G W R 94 31 A 16 G 15 * SNP after filtered 19,781 GK0005-001.fwd.pileup.snp.filtered head 3 GK0005-001.fwd.pileup.snp.filtered SNP position SNP call SNP qual dbSNP RefAlleles SNP call(fwd) Allele count(fwd) SNP call(rev) Allele count(rev) '''chr12:25537917''' T 157 rs923491 K - - A A,44 '''chr16:84539303''' S 49 rs12716753 S - - K T,6,G,15 '''chr2:44588941''' R 94 rs698775 R R A,16,G,15 - - * SNP called by Robert's pipeline 18,146 SNPs.GK0005001.txt chr12 '''25537917''' A AA homozygous - ss chr16 '''84539303''' CG TG heterozygous - ss chr2 '''44588941''' AG AG heterozygous + ss * SNPDB Assembly Genome_Build Chr Chr_Pos rs923491 --> GRCh37.p5 37.3 12 25537917 RefSNP Alleles: G/T (check) rs12716753 --> GRCh37.p5 37.3 16 84539303 RefSNP Alleles: C/G rs698775 --> GRCh37.p5 37.3 2 44588941 RefSNP Alleles: A/G * The results above revealed that the SNP called by both methods were consistent
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