Merge pull request #236 from deeptools/FAQ

added faq with HiCMatrix 12 to 13

docs/content/faq.rst

@@ -0,0 +1,15 @@
+FAQ
+===
+
+.. contents:: 
+    :local:
+
+Why the scale of my Hi-C plot suddenly changed
+----------------------------------------------
+pyGenomeTracks is using `HiCMatrix <https://github.com/deeptools/HiCMatrix>`_ to read the matrix from ``h5`` and ``cool`` format.
+From version 12 to version 13, a normalization step when reading ``cool`` file was removed. This normalization was mostly used 
+when you were providing ``cool`` file from `cooler balance <https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance>`_.
+
+If you want to keep the old scale you need to downgrade to HiCMatrix version 12 but version 13 also correct some bugs so we advice
+to change your ``max_value`` in your parameter file to adjust to the new scale.
+

docs/index.rst

@@ -47,4 +47,4 @@ Table of content
    content/possible-parameters
    content/adding-new-tracks
    content/releases
-
+   content/faq