From 35f3d0cb81f16eb581aef1b41417666332b83692 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Fri, 15 May 2020 17:26:02 +0200
Subject: [PATCH] added faq with HiCMatrix 12 to 13

---
 docs/content/faq.rst | 15 +++++++++++++++
 docs/index.rst       |  2 +-
 2 files changed, 16 insertions(+), 1 deletion(-)
 create mode 100644 docs/content/faq.rst

diff --git a/docs/content/faq.rst b/docs/content/faq.rst
new file mode 100644
index 00000000..5795679a
--- /dev/null
+++ b/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.
+
diff --git a/docs/index.rst b/docs/index.rst
index c33acc5e..4bda07bc 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -47,4 +47,4 @@ Table of content
    content/possible-parameters
    content/adding-new-tracks
    content/releases
-
+   content/faq