3C Analysis methods for Faryabi Lab

Hosted here are analysis / processing methods for Chromatin Conformtion Capture (3C) experiments.

• Faryabi Lab DockerHub
• Juicer
• Cooler
• hic2cool
• Homer
• GENOVA

Overview of methods included in this repository

/processing

• Workflows:
  • 3C processing (./Ingest_3C) - uses Juicer for initial alignment/processing/normalization, then converts to .(m)cool using hic2cool. First step to processing 3C data.
• make_homer_input.sh: Convert Juicer's merged_nodup.txt (or, really any file in AidenLab's "long" format) to a Homer-compatible format. This new input is then used to create a Tag Directory via Homer's makeTagDirectory.

/visualization

• A series of R scripts mainly using the GENOVA package to do basic analyses and plot 3C data.
         genova_loadCooler.R - Load a .cool/.mcool file as a GENOVA-compatible object for plotting.
         genova_viewMatrix.R - Preconfigured GENOVA commands for viewing single & differential matrics in a variety of formats.
         genova_aggregatePeakAnalysis.R - Calculate APA values and plot.

/quantify_matrix

• FetchPixelFromMatrixGivenBedpe.py: Given a matrix in .cool/.mcool form and a BEDPE file of interacting coordinates, extract raw and normalized contact counts.