Juicebox Visualization

Input Data Format

The Juicer Tools and Juicebox software is centered around the .hic file, a highly compressed binary file that provides rapid random access to the matrices at nested resolution levels. Juicer tool Pre can help us generate such .hic file from various input data format. We will use the simplest format for illustration.

Short format (cited from https://github.com/aidenlab/juicer/wiki/Pre) A whitespace separated file that contains, on each line

<str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2>

  • str = strand (0 for forward, anything else for reverse; we can ignore this option as currently strand information is not stored within .hic files.)

  • chr = chromosome (must be a chromosome in the genome)

  • pos = position

  • frag = restriction site fragment (We can ignore this option by putting a dummy value. Pre throws away reads that map to the same restriction fragment. If using dummy numbers for the frag field, be sure they are different for the different read ends; that is, should be 0 and should be 1.)

Data Preparation

To generate the short format interaction file, we can make use of AMSI_3Dgenomics/results/Ring/step4_duplicatesRemoval/Ring_chr7.validPairs.noDup which records the nonduplicated valid read pairs.

mkdir -p AMSI_3Dgenomics/results/Ring/Juicebox

awk -v OFS="\t" '{print 0, $2, $3, 1, 16, $7, $8, 0}' AMSI_3Dgenomics/results/Ring/step4_duplicatesRemoval/Ring_chr7.validPairs.noDup >AMSI_3Dgenomics/results/Ring/Juicebox/Ring_chr7.pre

.hic File Generation

Convert interactions (short format) into .hic format.

java -Xmx2g -jar AMSI_3Dgenomics/bin/juicer_tools_1.14.08.jar pre AMSI_3Dgenomics/results/Ring/Juicebox/Ring_chr7.pre AMSI_3Dgenomics/results/Ring/Juicebox/Ring_chr7.hic AMSI_3Dgenomics/Plasmodium/supportData/plasmodium.chrom.sizes -d true

Transfer AMSI_3Dgenomics/results/Ring/Juicebox/Ring_chr7.hic back to your own laptop for online visualization.

Visualization

  1. Open the Online Juicebox at https://aidenlab.org/juicebox/.

  2. Load Map - Local Map File - Find the downloaded .hic file.

  3. Check the following:

    • genome coordinate

    • resolution

    • color scale

    • Normalization (Optional task: compare KR normalization with the Balanced normalization function on Juicebox.)

    • Comparison between three stages

    • Public data and other genome tracks

    • Desktop version