From 214906b3587de33dd38cc112947aaa3c139c02fc Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Sun, 27 Jan 2013 16:27:44 -0500
Subject: [PATCH] update FAQ
---
docs/content/faq.rst | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/docs/content/faq.rst b/docs/content/faq.rst
index 8c704664..0088e2b6 100644
--- a/docs/content/faq.rst
+++ b/docs/content/faq.rst
@@ -103,3 +103,33 @@ To display the help for a specific tool (e.g., ``bedtools shuffle``), use:
-n Report the number of BED entries that were merged.
- Note: "1" is reported if no merging occurred.
+
+
+
+
+
+====================
+Issues with output
+====================
+
+------------------------------------------------------------------------
+I *know* there are overlaps, but none are reported. What might be wrong?
+------------------------------------------------------------------------
+
+There are two common causes of this problem. The first cause is non-obvious
+differences in the way chromosomes are named in files being compared.
+For example, "1" is not the same as "chr1" just as " chr1" is not the same
+as "chr1". Secondly, users often copy files from a Windows machine to a UNIX
+machine. This causes issues because Windows uses two bytes to represent
+the end of a line (``\r\n``) whereas the UNIX convention uses a single byte
+(``\n``). If your files don't conform to the UNIX convention, you will have
+problems. One can convert files from Windows to UNIX with
+the following command:
+
+.. code-block:: bash
+
+ perl -i -p -e 's/\r\n/\n/g;' file.windows > file.unix
+
+
+
+
--
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