.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_qc_pacbio.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_plot_qc_pacbio.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_plot_qc_pacbio.py:


read length histograms pacbio data
=====================================

QC pacbio example

.. GENERATED FROM PYTHON SOURCE LINES 10-12

First, let us get a data set example.
Note the .bam extension

.. GENERATED FROM PYTHON SOURCE LINES 12-16

.. code-block:: Python

    from sequana import sequana_data

    dataset = sequana_data("test_pacbio_subreads.bam")








.. GENERATED FROM PYTHON SOURCE LINES 17-18

Create a :class:`sequana.pacbio.BAMPacbio` instance

.. GENERATED FROM PYTHON SOURCE LINES 18-22

.. code-block:: Python

    from sequana.pacbio import PacbioSubreads

    qc = PacbioSubreads(dataset)








.. GENERATED FROM PYTHON SOURCE LINES 23-24

plot the histogram of read length

.. GENERATED FROM PYTHON SOURCE LINES 24-27

.. code-block:: Python

    qc.hist_read_length()





.. image-sg:: /auto_examples/images/sphx_glr_plot_qc_pacbio_001.png
   :alt: Read length    Mean length : 1405.68
   :srcset: /auto_examples/images/sphx_glr_plot_qc_pacbio_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    0it [00:00, ?it/s]
    130it [00:00, 24595.58it/s]




.. GENERATED FROM PYTHON SOURCE LINES 28-29

plot the histogram of the SNRs for each base

.. GENERATED FROM PYTHON SOURCE LINES 29-30

.. code-block:: Python

    qc.hist_snr()



.. image-sg:: /auto_examples/images/sphx_glr_plot_qc_pacbio_002.png
   :alt: plot qc pacbio
   :srcset: /auto_examples/images/sphx_glr_plot_qc_pacbio_002.png
   :class: sphx-glr-single-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 0.239 seconds)


.. _sphx_glr_download_auto_examples_plot_qc_pacbio.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_qc_pacbio.ipynb <plot_qc_pacbio.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_qc_pacbio.py <plot_qc_pacbio.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_qc_pacbio.zip <plot_qc_pacbio.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_