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.. "auto_examples/qc_report_example.py"
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.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_qc_report_example.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_qc_report_example.py:


QC Report
===========================

Outputs quality control report from given bam files.

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Usually as a first step after receiving bam files, we want to do a quality check
and assess our data. This code generates a PDF report of important QC statistics
for modified base data from Nanopore sequencing.

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1. Python option
----------------

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.. code-block:: default


    import dimelo as dm

    # first we specify the locations of our bam files
    bam = "winnowmap_guppy_merge_subset.bam"
    sampleName = "CTCF"
    outdir = "./out"

    # next we run the "qc_report" function
    dm.qc_report(bam, sampleName, outdir)
    # now our output directory will have a file called "CTCF_qc_report.pdf"


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2. Command line option
----------------
``dimelo-qc-report -f winnowmap_guppy_merge_subset.bam -s CTCF -o ./out``

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Output
----------------------
.. figure:: ../auto_examples/images/QC_Terminal_Output.png
.. figure:: ../auto_examples/images/CTCF_qc_report.png


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

   **Total running time of the script:** ( 0 minutes  0.000 seconds)


.. _sphx_glr_download_auto_examples_qc_report_example.py:


.. only :: html

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



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

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



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

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


.. only:: html

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