List up all visualizable genome data files recursivley under a specified web directory, and visualize them
(bed type files should be compressed with bgzip and indexed with tabix -p bed).
bam (with index .bai)
bed (interaction, tagAlign)
hammock (converted from narrowPeak, broadPeak and gappedPeak)
For bigwig, you don't need any conversion to visualize it, it's already compressed and indexed.
For bam, you need to have index (.bam.bai)
For bed type files (bed, bedGraph, bedpe, hammock, ...), they need to be compressed with 'bgzip' and indexed with 'tabix -p bed'.
If you don't have index for your bams and bed type files, use a converter provided in ./converter/recursive_gen_idx.sh
It will automatically and recursively bgzip/index/convert all genome data files listed above.
If you specify file extension as the second parameter, files only with that extension will be converted.
-color: hex color code (look for color hex codes at here)
bam, bed and interaction types have their own colors (according to the strand of reads or the sign of scores).
bigwig : blue
bedGraph : maroon
hammock : red
-name: by default track name is its filename.
IMPORTANT! : Do not leave any "undefined" types in the text area below. Specify an appropriate type for them.
track format: type,hex_color,name,URL
Extra tracks (same format: type,hex_color,name,URL).
Tracks defined here will be added at the end of the visualization session.
Color table for epigenome IDs and chromatin marks (including histones).
Overrides track colors if genome data file name contains epigenome IDs or chromatin mark names (ignoring all non-letter characters)
Colors for epigenome IDs come from Roadmap Epigenomics Metadata Sheets