I'm trying to create a new Custom Track for UCSC, but I'm not sure exactly how to do it.
I've gone through the tutorial and have made all sorts of tracks using it. But I'm really trying to make a specific type of track: not unlike the "Genome Position" track that comes as one of the default tracks: http://genome.ucsc.edu/trash/hgt/hgt_genome_4b02_5da90.png (See the track at the top)
I've looked into "Genome Graphs", "BedGraphs", "Wiggle files" to mention a few, but nothing I've found seems to allow me to make the boxes - with letters - of multiple colors on a base-by-base basis (lots of "bases" there :) ).
I thought one way to learn this might be to download the Base Position code (is it a "GenomeGraph", a BedGraph, or what?).
Does anyone know where I could find that code? Even better: does anyone know how to make those multi-colored boxes? I'd be thrilled just to know precisely what TYPE of track that is: might be able to figure it out from there!
Thanks 1x10^6!
Wyatt
There's a lot in the UCSC browser code that is not configurable by the custom track interface, and this seems to be one of them.
You might be able to fake something using one BED file for each coding frame, and then put them in dense mode and organize them next to each other. I don't know of a way to get letters inside the blocks, so you would need a custom color scheme to encode the information you care about.
What kind of data do you want to show? VCF and BAM files are able to show mismatches as letters, so you might be able to adapt those formats to your data.
This is some great advice to start with, Ryan! Thanks so much! I've been looking into the VCF and I'm wondering about those, but I hadn't thought about trying the BAM format. Off to a good start!