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Quickstart
==========
Install `pairtools` and all of its dependencies using the
`conda <https://conda.io/docs/user-guide/install/index.html>`_ package manager and
the `bioconda <https://bioconda.github.io/index.html>`_ channel for bioinformatics
software.
.. code-block:: bash
$ conda install -c conda-forge -c bioconda pairtools
Setup a new test folder and download a small Hi-C dataset mapped to sacCer3 genome:
.. code-block:: bash
$ 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:
.. code-block:: bash
$ 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:
.. code-block:: bash
$ pairtools parse -c sacCer3.reduced.chrom.sizes -o MATalpha_R1.pairs.gz --drop-sam MATalpha_R1.bam
Inspect the resulting table:
.. code-block:: bash
$ less MATalpha_R1.pairs.gz
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