.. _quickstart:

Quickstart
==========

For the impatient, just use ``portcullis full -t <threads> <genome> (<bam>)+`` 
to get up and running.  This runs the following subtools in order:

* Prepare
* Junction Analysis
* Junction Filtering
* Bam Filtering (optional)

This will output both unfiltered and filtered junctions from the provided BAM file.  However, we
recommend you read the :ref:`using` section for a more detailed description of
what each stage does.