> For the complete documentation index, see [llms.txt](https://ycl6.gitbook.io/methylation-sequencing-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ycl6.gitbook.io/methylation-sequencing-analysis/analysis_work_flow/dna_methylation_at_cpg_islands.md).

# DNA Methylation at CpG Islands

Same as Chapter 2.1, we used `intersectBed` and `groupBy` commands to calculate the average methylation values at each CpG island.

```
# Console output

# intersectBed 
chr1    18598   19673   CpG|116 216     +       chr1    18598   18599   0
chr1    18598   19673   CpG|116 216     +       chr1    18612   18613   0
chr1    18598   19673   CpG|116 216     +       chr1    18614   18615   0
chr1    18598   19673   CpG|116 216     +       chr1    18627   18628   0
chr1    18598   19673   CpG|116 216     +       chr1    18636   18637   0

# groupBy
chr1    18598   19673   116     0
chr1    124987  125426  30      0
chr1    317653  318092  29      0
chr1    427014  428027  84      0
chr1    439136  440407  99      0
```

```bash
cd ~/

bsub -q 16G -o stdout -e stderr "intersectBed -a Data/cpgIslandExt.bed.gz -b /work3/NRPB1219/hg18_h1_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 10,10 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/cpgIslandExt.h1.meth"

bsub -q 16G -o stdout -e stderr "intersectBed -a Data/cpgIslandExt.bed.gz -b /work3/NRPB1219/hg18_imr90_meth.bedGraph -wa -wb | groupBy -i - -g 1-3 -c 10,10 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,sprintf(\"%.4f\",\$5) }' > Output/cpgIslandExt.imr90.meth"
```

Use `bjobs` to check the all jobs have completed and `ls` to check the files was in the "Output" folder.

`ls -la ~/Output/cpgIslandExt.*.meth`

```
# Console output

-rw------- 1 s00yao00 s00yao00 960543 2014-12-20 17:45 /home/s00yao00/Output/cpgIslandExt.h1.meth
-rw------- 1 s00yao00 s00yao00 960543 2014-12-20 17:44 /home/s00yao00/Output/cpgIslandExt.imr90.meth
```