put helpful usage tips on main docs page
@@ -18,6 +18,15 @@ Tutorial
==========================
We have developed a fairly comprehensive `tutorial <http://quinlanlab.org/tutorials/bedtools/bedtools.html>`_ that demonstrates both the basics, as well as some more advanced examples of how bedtools can help you in your research. Please have a look.
+==========================
+Important notes
+==========================
+- With the exception of BAM files, `bedtools` assumes all input files are TAB delimited.
+- `bedtools` also assumes that all input files use UNIX line endings.
+- Unless you use the `-sorted` option, `bedtools` currently does not support chromosomes larger than 512Mb
+- When using the -sorted option with files whose chromosomes are not lexicographically sorted (e.g., sort -k1,1 -k2,2n for BED files), one must provide a genome file (`-g`) defining the expected chromosome order.
+
+
==========================
Interesting Usage Examples
==========================
