DNA Methylation at Various Genic Structure Regions
Again, we use intersectBed and groupBy commands to calculate the average methylation values at each designated region.
Intergenic Regions
# Console output
# intersectBed
chr1 0 1736 chr1 468 469 0
chr1 0 1736 chr1 470 471 0.666667
chr1 0 1736 chr1 483 484 0.5
chr1 0 1736 chr1 488 489 1
chr1 0 1736 chr1 492 493 0.857143
# groupBy
chr1 0 1736 97 0.19548
chr1 20972 24416 27 0
chr1 25944 42911 148 0.10567
chr1 44799 52810 39 0.56999
chr1 53750 58917 21 0.22781cd ~/
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.intergenic.bed.gz -b /work3/NRPB1219/hg18_h1_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 7,7 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/gencode.v3c.intergenic.h1.meth"
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.intergenic.bed.gz -b /work3/NRPB1219/hg18_imr90_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 7,7 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/gencode.v3c.intergenic.imr90.meth"Merged Promoter Regions
# Console output
# intersectBed
chr1 736 2372 chr1 747 748 0
chr1 736 2372 chr1 749 750 0
chr1 736 2372 chr1 765 766 0
chr1 736 2372 chr1 770 771 0
chr1 736 2372 chr1 776 777 0
# groupBy
chr1 736 2372 71 0
chr1 18416 20728 136 0
chr1 25436 26944 22 0
chr1 41911 43411 8 0.1875
chr1 51810 53310 14 0.65505cd ~/
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.promoter_merged.bed.gz -b /work3/NRPB1219/hg18_h1_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 7,7 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/gencode.v3c.promoter_merged.h1.meth"
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.promoter_merged.bed.gz -b /work3/NRPB1219/hg18_imr90_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 7,7 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/gencode.v3c.promoter_merged.imr90.meth"Merged Exonic Regions
# Console output
# intersectBed
chr1 1736 2090 chr1 1741 1742 0
chr1 1736 2090 chr1 1808 1809 0
chr1 1736 2090 chr1 1822 1823 0
chr1 2475 2584 chr1 2534 2535 0
chr1 2475 2584 chr1 2537 2538 0
# groupBy
chr1 1736 2090 3 0
chr1 2475 2584 3 0
chr1 3083 4692 32 0.0625
chr1 4832 4901 3 0
chr1 5658 5810 5 0cd ~/
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.exon_merged.bed.gz -b /work3/NRPB1219/hg18_h1_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 7,7 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/gencode.v3c.exon_merged.h1.meth"
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.exon_merged.bed.gz -b /work3/NRPB1219/hg18_imr90_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 7,7 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/gencode.v3c.exon_merged.imr90.meth"Intronic Regions
# Console output
# intersectBed
chr1 2090 2475 chr1 2127 2128 0
chr1 2090 2475 chr1 2133 2134 0
chr1 2090 2475 chr1 2140 2141 0
chr1 2090 2475 chr1 2167 2168 0
chr1 2090 2475 chr1 2180 2181 0
# groupBy
chr1 2090 2475 12 0
chr1 2584 2837 7 0
chr1 2915 3083 2 0.33333
chr1 4692 4832 3 0.41667
chr1 4901 5658 19 0cd ~/
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.intron_merged.bed.gz -b /work3/NRPB1219/hg18_h1_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 7,7 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/gencode.v3c.intron_merged.h1.meth"
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.intron_merged.bed.gz -b /work3/NRPB1219/hg18_imr90_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 7,7 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/gencode.v3c.intron_merged.imr90.meth"UTR Regions
# Console output
# intersectBed
chr1 1737 2090 5_UTR ENST00000456328 + chr1 1741 1742 0
chr1 1737 2090 5_UTR ENST00000456328 + chr1 1808 1809 0
chr1 1737 2090 5_UTR ENST00000456328 + chr1 1822 1823 0
chr1 2476 2584 5_UTR ENST00000456328 + chr1 2534 2535 0
chr1 2476 2584 5_UTR ENST00000456328 + chr1 2537 2538 0
# groupBy
chr1 1737 2090 5_UTR ENST00000456328 + 3 0
chr1 2476 2584 5_UTR ENST00000456328 + 3 0
chr1 3084 4021 3_UTR ENST00000456328 + 14 0.14286
chr1 4226 4561 3_UTR ENST00000438504 - 7 0
chr1 4226 4692 3_UTR ENST00000423562 - 15 0cd ~/
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.UTR.bed.gz -b /work3/NRPB1219/hg18_h1_meth.bedGraph -wa -wb | groupBy -i - -g 1-6 -c 10,10 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,\$5,\$6,\$7,sprintf(\"%.4f\",\$8) }' > Output/gencode.v3c.UTR.h1.meth"
bsub -q 16G -o stdout -e stderr "intersectBed -a Data/gencode.v3c.UTR.bed.gz -b /work3/NRPB1219/hg18_imr90_meth.bedGraph -wa -wb | groupBy -i - -g 1-6 -c 10,10 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,\$5,\$6,\$7,sprintf(\"%.4f\",\$8) }' > Output/gencode.v3c.UTR.imr90.meth"Check output files
Use bjobs to check the all jobs have completed and ls to check the files was in the "Output" folder.
ls -la ~/Output/gencode.v3c.*
# Console output
-rw------- 1 s00yao00 s00yao00 7640285 2014-12-20 18:23 /home/s00yao00/Output/gencode.v3c.exon_merged.h1.meth
-rw------- 1 s00yao00 s00yao00 7640285 2014-12-20 18:23 /home/s00yao00/Output/gencode.v3c.exon_merged.imr90.meth
-rw------- 1 s00yao00 s00yao00 1048190 2014-12-20 18:25 /home/s00yao00/Output/gencode.v3c.intergenic.h1.meth
-rw------- 1 s00yao00 s00yao00 1048190 2014-12-20 18:25 /home/s00yao00/Output/gencode.v3c.intergenic.imr90.meth
-rw------- 1 s00yao00 s00yao00 7621155 2014-12-20 18:25 /home/s00yao00/Output/gencode.v3c.intron_merged.h1.meth
-rw------- 1 s00yao00 s00yao00 7621155 2014-12-20 18:25 /home/s00yao00/Output/gencode.v3c.intron_merged.imr90.meth
-rw------- 1 s00yao00 s00yao00 2100589 2014-12-20 18:23 /home/s00yao00/Output/gencode.v3c.promoter_merged.h1.meth
-rw------- 1 s00yao00 s00yao00 2100589 2014-12-20 18:23 /home/s00yao00/Output/gencode.v3c.promoter_merged.imr90.meth
-rw------- 1 s00yao00 s00yao00 9696115 2014-12-20 18:36 /home/s00yao00/Output/gencode.v3c.UTR.h1.meth
-rw------- 1 s00yao00 s00yao00 9696115 2014-12-20 18:24 /home/s00yao00/Output/gencode.v3c.UTR.imr90.methLast updated