Conformation Analysis

There are many open-source tools available that enable researchers to perform conformation analyses on contact matrices. We aim to hightlight the tools and commands we use here at Cantata Bio call features. This is not a comprenisve list, nor do we own or manage any of the tools listed below. Please refer to their source document pages for more information or for help in trouble shooting the use of these tools. For each analysis performed below we provide, a link to the tool repo, the input file, the example command, and an example output for you to check your results against.

Example input files (.mcool and .hic files)

• Example mcool file

• Example hic file

A/B Compartments

Recommended Software

• Fanc-C https://fan-c.readthedocs.io/en/latest/

Example Command

fanc compartments -f -v TopoLink_eigen_64kb.bed -d TopoLink_AB_64kb.bed -g hg38.fa TopoLink.mcool@64000 TopoLink_64kb.ab

Example Output(s)

• Example AB compartments file

• Example AB compartments bed file

• Example AB Eigenvector file

Topologically Associated Domains

Recommended Software

• Juicer Arrowhead https://github.com/aidenlab/juicer

Example Command

java -jar -Xmx48000m  -Djava.awt.headless=true -jar juicer_tools.jar arrowhead --threads 16 -k KR -m 2000 -r 10000 TopoLink.hic TAD_calls
java -jar -Xmx48000m  -Djava.awt.headless=true -jar juicer_tools.jar arrowhead --threads 16 -k KR -m 2000 -r 5000 TopoLink.hic TAD_calls

Example Output(s)

• Example 10kb TADs file

• Example 5kb TADs file

Chromatin Loops

Recommended Software

• Mustache https://github.com/ay-lab/mustache

Example Command

mustache -p 48 -f TopoLink.mcool -r 16000 -o TopoLink_16000kb_loops.tsv
mustache -p 48 -f TopoLink.mcool -r 4000 -o TopoLink_4000kb_loops.tsv

Example Output(s)

• Example 16kb Loops file

• Example 4kb Loops file