.. _all_tutorials:

Tutorials
=========

.. toctree::
   :maxdepth: 1

   tutorial-cel
   existing-alignments
   tutorial-containers


The tutorials include a small test Ribo-seq dataset and reference output that is also used for regression tests. It has been constructed to include some reads which uniquely map to the annotated transcripts, some reads which map to ribosomal sequences, some reads which do not uniquely map to the genome, and some reads which are filtered due to quality issues.

Download the dataset
--------------------

`Click here <https://data.dieterichlab.org/s/kYn5sY7YrJPWDiG/download>`_ and unzip the archive. Navigate to the *c-elegans-chrI-example* directory.

Content
^^^^^^^

* *c-elegans-test.yaml* The YAML configuration file.
* *c-elegans.alignments-only.yaml* Another YAML configuration to explain :ref:`existing_alignment`.

**input**

* *c-elegans.test-chrI.rep-1.fastq.gz* Ribo-seq sample 1.
* *c-elegans.test-chrI.rep-2.fastq.gz* Ribo-seq sample 2.
* *WBcel235.chrI.fa* The reference sequence of Chromosome I for *C. elegans*.
* *WBcel235.79.chrI.gtf* The Ensembl, version 79 annotation, for Chromosome I for *C. elegans*.
* *X03680_1.fasta* The sequence of the ribosomal subunits for *C. elegans*. The reference accession is *X03680.1*.
* *riboseq-adapters.fa* An example adapter file. It includes typical TruSeq and ArtSeq adapters, as well as a few adapters from the literature. It also includes a custom adapter used to create the sample dataset.

**reference**

This directory contains reference genome annotations and predictions generated by **Rp-Bp**.