> 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/an_introduction_of_ucsc_genome_browser/the_compressed_binary_index_format.md).

# The Compressed Binary Index Format

Due to the time limitation, we will not demonstrate how to set up your own track hub to host private data. Please refer to the UCSC Help page if you want to know more on this topic:

* <http://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html>
* <http://genome.ucsc.edu/goldenPath/help/customTrack.html>

However, we will show here how to convert BED format to bigBed, and bedGraph to BigWIG. The file conversion process is necessary because UCSC Genome Browser only accepts compressed binary index formats that have smaller file sizes.

**Using `bedGraphToBigWig`**

```bash
cd ~/

bsub -q 16G -o stdout -e stderr "Tools/bedGraphToBigWig /work3/NRPB1219/hg18_h1_meth.bedGraph /work3/NRPB1219/chromInfo.txt Output/hg18_h1_meth.bw"

bsub -q 16G -o stdout -e stderr "Tools/bedGraphToBigWig /work3/NRPB1219/hg18_imr90_meth.bedGraph /work3/NRPB1219/chromInfo.txt Output/hg18_imr90_meth.bw"
```

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

`ls -la ~/Output/*.bw`

```
# Console output

-rw------- 1 s00yao00 s00yao00 269725108 2014-12-20 22:51 /home/s00yao00/Output/hg18_h1_meth.bw
-rw------- 1 s00yao00 s00yao00 272755992 2014-12-20 22:52 /home/s00yao00/Output/hg18_imr90_meth.bw
```

**Using `bedToBigBed`**

```bash
cd ~/

bsub -q 16G -o stdout -e stderr "Tools/bedToBigBed /work3/NRPB1219/hg18_h1_hmr.bed /work3/NRPB1219/chromInfo.txt Output/hg18_h1_hmr.bb"

bsub -q 16G -o stdout -e stderr "Tools/bedToBigBed /work3/NRPB1219/hg18_imr90_hmr.bed /work3/NRPB1219/chromInfo.txt Output/hg18_imr90_hmr.bb"
```

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

`ls -la ~/Output/*.bb`

```
# Console output

-rw------- 1 s00yao00 s00yao00  936059 2014-12-20 22:50 /home/s00yao00/Output/hg18_h1_hmr.bb
-rw------- 1 s00yao00 s00yao00 1330574 2014-12-20 22:50 /home/s00yao00/Output/hg18_imr90_hmr.bb
```


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