> 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_repeat_elements.md).

# DNA Methylation at Repeat Elements

The BED file containing the repeat element annotations (prepared in Chapter 1.3) was located in the `Data` folder. In the hg18 version of the RepMask 3.2.7 annotation, the repeat elements were categorized into 21 repeat classes (see **Table 2**). In this demonstration, we will calculate an compare the methylation levels of five types common repeats: SINE, LINE, LTR, Satellite and DNA.

**Table 2.** Number of features in each repeat class in the RepMask 3.2.7 annotation (build hg18)

| No. of Entries | Repeat Classes  |
| -------------- | --------------- |
| *1757823*      | *SINE*          |
| *1468898*      | *LINE*          |
| *699087*       | *LTR*           |
| *454482*       | *DNA*           |
| 407205         | Simple\_repeat  |
| 364098         | Low\_complexity |
| 6998           | Unknown         |
| *6096*         | *Satellite*     |
| 4251           | snRNA           |
| 3589           | Other           |
| 2204           | RC              |
| 1871           | DNA?            |
| 1751           | tRNA            |
| 1715           | rRNA            |
| 1437           | srpRNA          |
| 1296           | scRNA           |
| 715            | RNA             |
| 417            | SINE?           |
| 123            | LTR?            |
| 93             | Unknown?        |
| 52             | LINE?           |

Like before, we use `intersectBed` and `groupBy` commands to calculate the average methylation values at each repeat element from the five repeat classes.

```
# Console output

# intersectBed
chr1    468     1310    Satellite       0       -       telo    TAR1    chr1    468     469     0
chr1    468     1310    Satellite       0       -       telo    TAR1    chr1    470     471     0.666667
chr1    468     1310    Satellite       0       -       telo    TAR1    chr1    483     484     0.5
chr1    468     1310    Satellite       0       -       telo    TAR1    chr1    488     489     1
chr1    468     1310    Satellite       0       -       telo    TAR1    chr1    492     493     0.857143

# groupBy
chr1    468     1310    Satellite       89      0.21305
chr1    1540    1643    DNA     1       0
chr1    5128    5208    SINE    1       0
chr1    8769    8911    LINE    2       0
chr1    9877    10268   LINE    8       0
```

```bash
cd ~/

bsub -q 16G -o stdout -e stderr "intersectBed -a Data/hg18.rmskRM327.bed.gz -b /work3/NRPB1219/hg18_h1_meth.bedGraph -wa -wb | grep -Pw \"Satellite|DNA|LTR|LINE|SINE\" | groupBy -i - -g 1-4 -c 12,12 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,\$5,sprintf(\"%.4f\",\$6) }' > Output/hg18.rmskRM327.h1.meth"

bsub -q 16G -o stdout -e stderr "intersectBed -a Data/hg18.rmskRM327.bed.gz -b /work3/NRPB1219/hg18_imr90_meth.bedGraph -wa -wb | grep -Pw \"Satellite|DNA|LTR|LINE|SINE\" | groupBy -i - -g 1-4 -c 12,12 -o count,mean | awk -F $'\t' 'BEGIN { OFS=FS } { print \$1,\$2,\$3,\$4,\$5,sprintf(\"%.4f\",\$6) }' > Output/hg18.rmskRM327.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.rmskRM327.*.meth`

```
# Console output

-rw------- 1 s00yao00 s00yao00 119358409 2014-12-20 19:57 /home/s00yao00/Output/hg18.rmskRM327.h1.meth
-rw------- 1 s00yao00 s00yao00 119358409 2014-12-20 19:57 /home/s00yao00/Output/hg18.rmskRM327.imr90.meth
```