.. _doc:

Documentation
=============

Pipeline overview
~~~~~~~~~~~~~~~~~

.. automodule:: Xpression
    :members: xpression

Step 1 - Extract quality reads by barcode
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: extract_reads_from_pools
    :members: extract_reads_from_pools, write_results, extract_reads

Step 2 - Map quality read to reference
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Reads with ``good`` quality are mapped to the reference genome by `bwa`.

Step 3 - Count reads per locus
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: count_reads_per_region
    :members: count_reads_per_region

.. automodule:: create_gene_annotation_pickle
    :members:

Glossary:
==========

.. glossary::

   raw
    Number of reads counted within a locus.
  
   pM
    `reads per million` is :term:`raw` reads normalised to the factor of (total unique reads / 1 million reads). The number used is reported from step 2 as ``unique reads`` in the mapping_statistic.txt table for each sample.

   pKM
    `reads per kilobase-million` is :term:`pM` reads additionally normalised to the factor of (loci length / 1000 bp).