Tutorials
=========
Tutorials are divided into two sections:

 - The :ref:`examples-cookbook` contains step-by-step instructions for
   performing common tasks, with detailed explanations of each step
  
 - :ref:`examples-concepts` includes longer discussions of issues that arise
   in :term:`high-throughput sequencing` and genomics, and includes code
   examples when appropriate. 
  
We suggest downloading the :doc:`test_dataset` and following along.

 
.. _examples-cookbook:

Cookbook
--------

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============================================================================    ===========================================================================================
**Tutorial**                                                                    **Contents**
----------------------------------------------------------------------------    -------------------------------------------------------------------------------------------
:doc:`/examples/a1_genome_setup`                                                Set up a genome for downstream analysis, using :data:`plastid` or other toolkits

:doc:`/examples/a2_sample_processing`                                           Simplified workflow of how to align sequencing data

:doc:`/examples/count_vector`                                                   Retrieve a vector of :term:`high-throughput sequencing` :term:`counts`
                                                                                at each position in a transcript

:doc:`/examples/sequence`                                                       Fetch the sequences of regions of interest (e.g. transcripts) from a genome

:doc:`Gene expression & translation efficiency </examples/gene_expression>`     Compute gene expression measurements and translation efficicency using
                                                                                :term:`RNA-seq` & :term:`ribosome profiling`, and prepare
                                                                                data for differential expression analysis

:doc:`/examples/using_masks`                                                    Exclude specific regions -- for example, repetitive genome sequence
                                                                                that gives rise to :term:`multimapping` reads -- from analysis.
                                                                                Discussion of :term:`mask files <mask file>`.

:doc:`/examples/make_annotation`                                                Make a `BED`_, `BigBed`_, `GTF2`_, or `GFF3`_ file containing
                                                                                custom :term:`features <feature>`.

:doc:`Metagene analysis </examples/metagene>`                                   Perform :term:`metagene analysis <metagene>`, using :term:`ribosome profiling`
                                                                                data at the start codon as an example. Then, develop metagene analysis around
                                                                                a custom landmark for use with other data types

:doc:`Ribosomal P-site offsets </examples/p_site>`                              Determine a :term:`P-site offset` from :term:`ribosome profiling` data

:doc:`/examples/phasing`                                                        Estimate :term:`read phasing (triplet periodicity) <sub-codon phasing>`
                                                                                of :term:`ribosome profiling` data

:doc:`/examples/z_plotting`                                                     Demos of plotting tools in :mod:`plastid.plotting`
============================================================================    ===========================================================================================


.. _examples-concepts:
 
In-depth
--------

===============================================================    ===========================================================================================
**Tutorial**                                                       **Contents**
---------------------------------------------------------------    -------------------------------------------------------------------------------------------
:doc:`/concepts/data`                                              Introduction & discussion to the types of data used in genomics, 
                                                                   and the advantages and disadvantages of their various file formats

:doc:`/concepts/coordinates`                                       Primer on the various coordinate systems used in genomics

:doc:`/concepts/multimappers`                                      Issues arising when and strategies for handling :term:`multimapping` reads

:doc:`/concepts/mapping_rules`                                     In-depth discussion of :term:`mapping rules <mapping rule>`, with code examples
                                                                   of how to write your own :term:`mapping rule` for your own sequencing data type
===============================================================    ===========================================================================================


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