Install pairtools and all of its dependencies using the conda package manager and the bioconda channel for bioinformatics software.

$ conda install -c conda-forge -c bioconda pairtools

Setup a new test folder and download a small Hi-C dataset mapped to sacCer3 genome:

$ mkdir /tmp/test-pairtools
$ cd /tmp/test-pairtools
$ wget https://github.com/open2c/distiller-test-data/raw/master/bam/MATalpha_R1.bam

Additionally, we will need a .chromsizes file, a TAB-separated plain text table describing the names, sizes and the order of chromosomes in the genome assembly used during mapping:

$ wget https://raw.githubusercontent.com/open2c/distiller-test-data/master/genome/sacCer3.reduced.chrom.sizes

With pairtools parse, we can convert paired-end sequence alignments stored in .sam/.bam format into .pairs, a TAB-separated table of Hi-C ligation junctions:

$ pairtools parse -c sacCer3.reduced.chrom.sizes -o MATalpha_R1.pairs.gz --drop-sam MATalpha_R1.bam

Inspect the resulting table:

$ less MATalpha_R1.pairs.gz