.. _tutorials:

**********************
Tutorials
**********************

.. currentmodule:: HTSeq

This page contains a few tutorials to help you familiarize yourself with ``HTSeq``, including ``htseq-count`` and its barcode sibiling ``htseq-count-barcodes``.

Parsers
--------
- :ref:`tutorial_fastx`: Simple tutorial on hadling fasta and fastq files with ``HTSeq``.
- :ref:`tutorial_bam`: Simple tutorial on handling SAM/BAM/CRAM files.
- :ref:`step_vs_stretch`: Explanation of the different data structures used to store sparse genomic data.

Workflows
---------
- :ref:`tss`: TSS example for the ``HTSeq`` API
- :ref:`tutorial_highc`: Chromatin conformation example for the ``HTSeq`` API

Scripts
-------
- :ref:`tutorial_htseq`: Explanation of the inner workings of ``htseq-count``
- :ref:`tutorial_htseq_exon`: Calling ``htseq-count`` at the exon level.


.. toctree::
   :glob:
   :maxdepth: 1
   :titlesonly:
   :hidden:

   tutorials/fastx_reader
   tutorials/bam_reader
   tutorials/step_vs_stretch_vector
   tutorials/tss
   tutorials/highc
   tutorials/exon_example
   tutorials/tutorial_exon_level

