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mention atac mode
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rob-p committed Dec 7, 2024
1 parent 8771e65 commit db55332
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4 changes: 4 additions & 0 deletions docs/source/atac.rst
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atac
====

The ``atac`` command exposes the functionality of ``alevin-fry`` for processing RAD files containing scATAC-seq data. The ``atac`` command sets the *mode* of ``alevin-fry``, and this command itself takes one of several various sub-commands (``generate-permit-list`` and ``sort`` being the primary ones).
3 changes: 2 additions & 1 deletion docs/source/commands.rst
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The ``alevin-fry`` program exposes a number of different commands that are responsible for exposing different capabilities and performing different steps of the processing pipeline. The list of current and valid are documented below.

.. toctree::
atac
generate_permit_list
collate
quant
infer
infer
4 changes: 2 additions & 2 deletions docs/source/index.rst
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===================

Alevin-fry is a program exposing a suite of tools for single-cell sequencing analysis.
It makes use of the selective-alignment and tag processing framework of
`alevin <https://github.com/COMBINE-lab/salmon/>`_.
It makes use of the lightweight mapping and tag processing framework of
`piscem <https://github.com/COMBINE-lab/piscem/>`_.


.. toctree::

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