Welcome to TopoLink documentation

Overview

• Cantata Bio™ TopoLink® Loop Calling Kit is designed for the rapid generation of genomic interaction data, or Hi-C-like data. This workflow enables researchers to go from sample prep to a sequencing ready library in under one day.

• Key benefits of TopoLink:

  • Compressed overall workflow to single day compared to 2-5 day workflow of other Hi-C approaches

  • Reduced the sample input to 500 thousand cells from the 2-10 million cells required for Hi-C

  • Improved mapping rate and even genomic coverage result in more complete contact matrices

  • More complete matrices lead to a higher rate of discovery in conformation feature calling, e.g. TADs and Loops

• This guide will take you step by step on how to process and QC your TopoLink library, how to interpret the QC results, how to generate contact maps, and how to perform chromatin conformation feature calling. If you don’t yet have a sequencing TopoLink library and you want to get familiar with the data, you can download TopoLink sequence libraries from our publicly available data sets.

• The QC process starts with aligning the reads to a reference genome then retaining high quality mapped reads. From there the mapped data will be used to generate a pairs file with pairtools, which categorizes pairs by read type and insert distance, this step both flags and removes PCR duplicates. Once pairs are categorized, counts of each class are summed and reported.

• If this is your first time following this tutorial, please check the Before you begin page first.

Contents:

• Before you begin
  • Have a copy of the TopoLink scripts on your machine:
  • Dependencies
  • Input files
• Pre-Alignment
• From fastq to final valid pairs bam file
  • fastq to final valid pairs bam file - step by step
• Alignment and Proximity-Ligation QC
  • Complexity
  • QC Assessment
  • Sequencing Recommendations
• Generating Contact Matrix
  • Generating HiC contact maps using Juicer tools
  • Generating cooler contact maps
• Conformation Analysis
  • Example input files (.mcool and .hic files)
  • A/B Compartments
  • Topologically Associated Domains
  • Chromatin Loops
• TopoLink Data Sets
• Support

Indices and tables

• Index

• Module Index

• Search Page