> 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_tfbs.md).

# DNA Methylation at TFBS

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

```
# Console output

# intersectBed 
chr1    81184   81397   Rad21   1000    +       chr1    81320   81321   0
chr1    81184   81397   Rad21   1000    +       chr1    81334   81335   0
chr1    227464  227809  Rad21   602     +       chr1    227650  227651  0
chr1    227464  227809  Rad21   602     +       chr1    227656  227657  0
chr1    227464  227809  Rad21   602     +       chr1    227664  227665  0

# groupBy
chr1    81184   81397   Rad21   2       0
chr1    227464  227809  Rad21   5       0.1
chr1    227505  227800  CTCF    5       0.1
chr1    530491  530823  c-Myc   26      0.26923
chr1    535929  536126  Rad21   13      0.15385
```

```bash
cd ~/

bsub -q 16G -o stdout -e stderr "intersectBed -a Data/wgEncodeRegTfbsClustered.bed.gz -b /work3/NRPB1219/hg18_h1_meth.bedGraph -wa -wb | groupBy -i - -g 1-4 -c 10,10 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,\$5,sprintf(\"%.4f\",\$6) }' > Output/wgEncodeRegTfbsClustered.h1.meth"

bsub -q 16G -o stdout -e stderr "intersectBed -a Data/wgEncodeRegTfbsClustered.bed.gz -b /work3/NRPB1219/hg18_imr90_meth.bedGraph -wa -wb | groupBy -i - -g 1-4 -c 10,10 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,\$5,sprintf(\"%.4f\",\$6) }' > Output/wgEncodeRegTfbsClustered.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/wgEncodeRegTfbsClustered.*.meth`

```
# Console output

-rw------- 1 s00yao00 s00yao00 15299532 2014-12-20 18:18 /home/s00yao00/Output/wgEncodeRegTfbsClustered.h1.meth
-rw------- 1 s00yao00 s00yao00 15299532 2014-12-20 18:18 /home/s00yao00/Output/wgEncodeRegTfbsClustered.imr90.meth
```