Add faq section to docs

docs/faq.rst

@@ -0,0 +1,15 @@
+##########################
+Frequently Asked Questions
+##########################
+
+***************************
+Why is `chess sim` so slow?
+***************************
+A common cause for long runtimes of `chess sim` is when the input files are
+in `Cooler <https://github.com/mirnylab/cooler>`_ format. `chess sim` compares
+observed/expected transformed matrices, and these are often not precomputed
+and stored in this format. If your runs spend a long time in the 
+"INFO Loading query contact data" step, consider converting your data to
+`Juicer <https://github.com/aidenlab/juicer>`_, or `FANC <https://github.com/vaquerizaslab/fanc>`_ 
+format, as these usually store observed/expected values
+(see `here <https://fan-c.readthedocs.io/en/latest/fanc-executable/compatibility.html#cooler-cool-and-mcool>`_).

docs/index.rst

@@ -11,6 +11,7 @@ Welcome to chess-hic's documentation!
 
    Getting started with chess-hic <getting_started>
    The chess-hic command line tool <cli>
+   FAQ <faq>