Creating stranded signal tracks for the UCSC Genome Browser

Recently, I was asked by one of my collegues if there was a way to display stranded wiggle signal files. A couple of years ago I would say that it is possible, however quite messy, as the only way to display stranded wiggle signal files was to split the original genomic co-ordinate file (BED, SAM) per strand and then create two separate wiggle (or bigWig) tracks. This was happening because the wiggle (and later bedGraph) specification does not allow for overlapping signals. Now it is much clearer (slighlty more complicated though) by using the ability of the UCSC Genome Browser to overlay tracks, by creating a super/parent tracks and assigning children tracks to it. Unfortunately, this ability is only possible with┬átrack hubs.

In this post, I will show you how to create stranded wiggle (or in this example, bigWig) files by setting up a track hub that will host your signal files and which you can upload to the genome browser. For additional information on creating a track hub and the checks that have to be made before loading it, see this post and the script attached to it. Apart from your original track (this example uses an initial BED track, mapped to the hg18 human genome), you will need the following tools:

The┬ákent utilities┬áfrom UCSC
The┬áBED tools

The following commands and text files should help you achieve your goal:

/path/to/BEDTools/genomeCoverageBed -i my_file.bed -g /path/to/BEDTools/genomes/human.hg18.genome -bg -strand + > my_file_plus.bed
/path/to/BEDTools/genomeCoverageBed -i my_file.bed -g┬á/path/to/BEDTools/genomes/human.hg18.genome -bg -strand - | awk '{ print $1"\t"$2"\t"$3"\t-"$4 }' > my_file_minus.bed

/path/to/kent_source/bedGraphToBigWig my_file_plus.bed hg18.chrom.size my_file_plus.bigWig
/path/to/kent_source/bedGraphToBigWig my_file_minus.bed hg18.chrom.size my_file_minus.bigWig

The hg18.chrom.size text file contains simply the size of each chromosome can be downloaded using the fetchChromSizes tool from kent source:

/path/to/kent_source/fetchChromSizes hg18

The next step is to follow the instructions about track hubs┬áand create the directory structure described in the help page. In our case, the hub.txt file would be:

hub My_Stranded_Hub
shortLabel Stranded Signal
longLabel A custom track that displays stranded signal
genomesFile genomes.txt
email admin@yourdomain.com

The┬ágenomes.txt┬áfile would be:

genome hg18
trackDb hg18/trackDb.txt

and the trackDb.txt file would be:

track strandedSignal
container multiWig
aggregate transparentOverlay
showSubtrackColorOnUi on
shortLabel stranded
longLabel An example of stranded wiggle signal
boxedCgf on
type bigWig

┬á ┬á ┬á ┬á track myFilePlus
┬á ┬á ┬á ┬á parent strandedSignal
┬á ┬á ┬á ┬á type bigWig
┬á ┬á ┬á ┬á bigDataUrl http://your_bigdata_server/hg18/my_file_plus.bigWig
┬á ┬á ┬á ┬á color 180,0,0

┬á ┬á ┬á ┬á track myFileMinus
┬á ┬á ┬á ┬á parent strandedSignal
┬á ┬á ┬á ┬á type bigWig
┬á ┬á ┬á ┬á bigDataUrl http://your_bigdata_server/hg18/my_file_minus.bigWig
┬á ┬á ┬á ┬á color 0,180,0

Finally, you have to load the following custom hub:

http://your_bigdata_server/hub.txt