> 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_genomic_bins.md).

# DNA Methylation at Genomic Bins

For each one of the 500 bins, we use the `intersectBed` program of the bedtools utilities to compare the `bins.bed` file and `meth.bedGraph` files base-by-base. The output is piped into `groupBy` to calculate the number of features being joined (in this case is the methylation values at CpG) and the average methylation level for each bin (i.e. `-c 7,7 -o count,mean`). Lastly, `awk` was used to print the methylation levels in four decimal places.

```
# Console output

# intersectBed
chr1    0       494500  chr1    468     469     0
chr1    0       494500  chr1    470     471     0.666667
chr1    0       494500  chr1    483     484     0.5
chr1    0       494500  chr1    488     489     1
chr1    0       494500  chr1    492     493     0.857143

# groupBy
chr1    0       494500  3973    0.051545
chr1    494500  989000  11539   0.29057
chr1    989000  1483500 19948   0.28879
chr1    1483500 1978000 16014   0.4603
chr1    1978000 2472500 17089   0.47023

# awk
chr1    0       494500  3973    0.0515
chr1    494500  989000  11539   0.2906
chr1    989000  1483500 19948   0.2888
chr1    1483500 1978000 16014   0.4603
chr1    1978000 2472500 17089   0.4702
```

```bash
cd ~/

bsub -q 16G -o stdout -e stderr "intersectBed -a Data/hg18.500bins.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/hg18.500bins.h1.meth"

bsub -q 16G -o stdout -e stderr "intersectBed -a Data/hg18.500bins.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/hg18.500bins.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/hg18.500bins.*.meth`

```
# Console output

-rw------- 1 s00yao00 s00yao00 737091 2014-12-20 16:26 /home/s00yao00/Output/hg18.500bins.h1.meth
-rw------- 1 s00yao00 s00yao00 737091 2014-12-20 16:26 /home/s00yao00/Output/hg18.500bins.imr90.meth
```