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

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

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