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==Penn African mQTL== ./mQTL_2MB_plink.pl ../PennAfrican_Batch1_genotypes ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > results.txt & *Remember that tfam file must have extra "phenotype" column of values "-9" ('missing') for plink to work! Divided high variance methylation matrix (77563 CpGs) to 8 groups: 2176 head -30000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_20001_30000/UPenn46_hg19_methylMatrix_filtered_20001-30000.txt 2179 head -40000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_30001_40000/UPenn46_hg19_methylMatrix_filtered_30001-40000.txt 2180 head -50000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_40001_50000/UPenn46_hg19_methylMatrix_filtered_40001-50000.txt 2181 head -60000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_50001_60000/UPenn46_hg19_methylMatrix_filtered_50001-60000.txt 2182 head -70000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_60001_70000/UPenn46_hg19_methylMatrix_filtered_60001-70000.txt 2183 tail -7573 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_70001_77573/UPenn46_hg19_methylMatrix_filtered_70001-77573.txt '''I found out that the PennAfrican_Batch1_genotypes file has SNP positions in build 36.3 and not in build 37.1''' '''Wrote script to lift over snp's RS values to hg19 positions''' [[File:liftOverRSvalues.txt]] After using liftover, I found that there were multiple occurrences of the same SNPs in snp132.txt file. wc -l PennAfrican_Batch1_genotypes_hg19.tped = 1109770 SNPs PennAfrican_Batch1_genotypes.tped = 1083730 SNPs Example of duplicated RS numbers in snp132.txt : 1266 chr2 89309681 89309682 rs3210114 0 - C C A/G cDNA single by-cluster 0 0 unknown exact 3 MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE, 0 1266 chr2 89345689 89345690 rs3210114 0 - C C A/G cDNA single by-cluster 0 0 unknown exact 3 MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE, 0 1267 chr2 89513110 89513111 rs3210114 0 - C C A/G cDNA single by-cluster 0 0 unknown exact 3 MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE, 0 1268 chr2 89619585 89619586 rs3210114 0 - T T A/G cDNA single by-cluster 0 0 unknown exact 3 MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE, 0 1270 chr2 89901585 89901586 rs3210114 0 + A A A/G cDNA single by-cluster 0 0 unknown exact 3 MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE, 0 1271 chr2 90007949 90007950 rs3210114 0 + G G A/G cDNA single by-cluster 0 0 unknown exact 3 MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE, 0 1273 chr2 90193220 90193221 rs3210114 0 + G G A/G cDNA single by-cluster 0 0 unknown exact 3 MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE, 0 *'''Some rs were also mapped to gapped regions in hg19 and to the multiple haplotypes of chr6.''' *'''Rewrote mQTL_2MB_plink.txt to build the tped files for each CpG''' Divided high variance methylation matrix (77563 CpGs) to 16 groups: 2472 head -5001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_1_5000/methylMat.txt 2473 head -10001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_5001_10000/methylMat.txt 2474 head -15001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_10001_15000/methylMat.txt 2475 head -20001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_15001_20000/methylMat.txt 2476 head -25001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_20001_25000/methylMat.txt 2477 head -30001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_25001_30000/methylMat.txt 2478 head -35001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_30001_35000/methylMat.txt 2479 head -40001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_35001_40000/methylMat.txt 2480 head -45001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_40001_45000/methylMat.txt 2481 head -50001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_45001_50000/methylMat.txt 2482 head -55001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_50001_55000/methylMat.txt 2483 head -60001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_55001_60000/methylMat.txt 2484 head -65001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_60001_65000/methylMat.txt 2485 head -70001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_65001_70000/methylMat.txt 2486 head -75001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_70001_75000/methylMat.txt 2487 tail -2575 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_75001_77573/methylMat.txt Added headers: 2491 cat header.txt no_1_5000/methylMat.txt > tmp 2492 mv tmp no_1_5000/methylMat.txt 2494 cat header.txt no_5001_10000/methylMat.txt > tmp 2495 mv tmp no_5001_10000/methylMat.txt 2497 cat header.txt no_10001_20000/methylMat.txt > tmp 2498 mv tmp no_10001_15000/methylMat.txt 2500 cat header.txt no_15001_20000/methylMat.txt > tmp 2501 mv tmp no_15001_20000/methylMat.txt 2502 cat header.txt no_20001_25000/methylMat.txt > tmp 2503 mv tmp no_20001_25000/methylMat.txt 2504 cat header.txt no_25001_30000/methylMat.txt > tmp 2505 mv tmp no_25001_30000/methylMat.txt 2506 cat header.txt no_30001_35000/methylMat.txt > tmp 2507 mv tmp no_30001_35000/methylMat.txt 2508 cat header.txt no_35001_40000/methylMat.txt > tmp 2509 mv tmp no_35001_40000/methylMat.txt 2510 cat header.txt no_40001_45000/methylMat.txt > tmp 2511 mv tmp no_40001_45000/methylMat.txt 2512 cat header.txt no_45001_50000/methylMat.txt > tmp 2513 mv tmp no_45001_50000/methylMat.txt 2514 cat header.txt no_50001_55000/methylMat.txt > tmp 2515 mv tmp no_50001_55000/methylMat.txt 2516 cat header.txt no_55001_60000/methylMat.txt > tmp 2517 mv tmp no_55001_60000/methylMat.txt 2518 cat header.txt no_60001_65000/methylMat.txt > tmp 2519 mv tmp no_60001_65000/methylMat.txt 2520 cat header.txt no_65001_70000/methylMat.txt > tmp 2521 mv tmp no_65001_70000/methylMat.txt 2522 cat header.txt no_70001_75000/methylMat.txt > tmp 2523 mv tmp no_70001_75000/methylMat.txt 2524 cat header.txt no_75001_77573/methylMat.txt > tmp 2525 mv tmp no_75001_77573/methylMat.txt In each folder: ../mQTL_2MB_plink.pl ../PennAfrican_Batch1_genotypes_hg19 methylMat.txt > results.txt & [[File:mQTL_2MB_plink.txt]] Script to create WIG and BED files for CpG-SNP interactions [[File:createBEDandWIGtracks.txt]] File of all CpG-SNP (Benjamini p-val < 0.05) [[File:combined_CpG-SNP_results.txt]] Files for chromosome 21 generated: [[File:chr21.dist.WIG.txt]] [[File:chr21.legend.BED.txt]] [[File:chr21.numCpGs.BED.txt]] [[File:chr21.p_val.BED.txt]] ===Plots of SNPs and their correlated CpGs, distances are in Mbp=== *Plot of CpG-SNPs on chromosome 21 [[File:African-mQTL-chr21.png]] *Plot of intergenic CpG-SNPs on chromosome 21 [[File:African-mQTL-chr21-snp-intergenic.png]] *Plot of intragenic CpG-SNPs on chromosome 21 [[File:African-mQTL-chr21-snp-intragenic.png]] *Plot of intragenic CpG-SNPs on chromosome 21 with high number of correlated CpGs [[File:African-mQTL-chr21-snp-intragenic-highCG.png]]
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