another usage tip in main docs
@@ -25,7 +25,7 @@ Important notes
- `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.
-
+- `bedtools` requires that chromosome naming schemes are identical in files that you are comparing (e.g., 'chr1' in one file and '1' in another won't work).
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Interesting Usage Examples
