Running the allele specific expression (ASE) pipeline
================================================================================

This workflow will perform all of the steps required to identify genes exhibiting allelic imballance. 

It will retrieve read data from the SRA, or use simulated datasets produced by the simulate reads pipeline

.. note::

   while the software can also process arbitrary fastq files (as long as they are paired), please note 
   that it will not be able to construct a report

All log files will be found in the ``logs`` directory at the end of the run.


Edit the file targets.txt
--------------------------------------------------------------------------------

manually edit the file targets.txt, placing one accession number per line, e.g.

::

   ERR2352620
   ERR2352630
   ERR2352640
   ERR2352650
   ERR2352660
   ERR2352670

Alternatively, if you have run the simulate reads pipeline, you can specify 
simulated data as follows:

::

   simulation_1_x1
   simulation_1_x2

Make sure the names correspond to the prefix of paired fastq files in the reads directory, e.g.

::

   reads/simulation_1_x1.1.fastq.gz
   reads/simulation_1_x1.2.fastq.gz
   reads/simulation_1_x2.1.fastq.gz
   reads/simulation_1_x2.2.fastq.gz

Modifying workflow parameters
--------------------------------------------------------------------------------

If desired, manually edit the file ``aliseq_params.json``


Running the workflow
--------------------------------------------------------------------------------

launch the workflow with:

.. code-block:: bash

   bash ../ALISEQ/aliseq.sh

.. note::

   If you encounter the following error mesage (e.g. after a power failure or loss of network connection) ``Error: Directory cannot be locked...``, run the following cmd before retrying
   
   .. code-block:: bash

      snakemake --unlock -s ../ALISEQ/scripts/workflow.snk