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updates documentation to reflect installation options
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Tom Smith
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Apr 22, 2016
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@@ -7,28 +7,38 @@ This repository contains tools for dealing with Unique Molecular Identifiers (UM | |
UMIs are removed and appended to the read name. Any other barcode, for example a library barcode, is left on the read. | ||
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* dedup: Implements a number of different UMI deduplication schemes. | ||
The recommended methods are `directional_adjecency` and `adjecency`. In general `directional_adjecency` seems to be less sensitive to starting conditions, but there are situations where `adjacency` might out perform. | ||
The recommended method is `directional_adjecency`. | ||
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See simulation results at the `CGAT blog <https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-the-solution-and-the-proof/>`_. | ||
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`Genome Science 2015 poster <http://f1000research.com/posters/4-728>`_. | ||
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Preprint on the way shortly... | ||
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Installation | ||
------------ | ||
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Clone git repository: | ||
If you're using Conda, you can use: | ||
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.. code:: bash | ||
git clone [email protected]:CGATOxford/UMI-tools.git | ||
conda install -c https://conda.anaconda.org/toms umi_tools | ||
Enter repository and run: | ||
Or pip: | ||
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.. code:: bash | ||
python setup.py develop | ||
pip install umi_tools | ||
Or if you'd like to work directly from the git repository: | ||
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.. code:: bash | ||
git clone [email protected]:CGATOxford/UMI-tools.git | ||
Enter repository and run: | ||
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.. code:: bash | ||
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