Added VERSION and spruced up USAGE_EXAMPLES

README

@@ -10,6 +10,14 @@ http://people.virginia.edu/~arq5x/bedtools.html
 BEDTools, prosaic as it may be, is a collection of utilities for comparing and 
 intersecting genomic features in the UCSC Genome Browser BED format. 
 
+===Installation===
+1.  If you are reading this, you successfully downloaded and unzipped/unpacked the source tarball.  Great.
+2.  Type "make all" at the command line.
+3.  If you encountered no errors, then all of the BED Tools should now be in bin/
+	If not, try to troubleshoot then email me: aaronquinlan@gmail.com
+4.  Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
+5.  Use the tools.
+
 
 ===Acknowledgments=== 
 1.  Jim Kent, UCSC.  
@@ -32,15 +40,6 @@ Discussion between Ira and I are largely the motivation for these tools.  We are
 down impromptu ideas and these tools were largely designed to facilitate tangents.
 
 
-===Installation===
-1.  If you are reading this, you successfully downloaded and unzipped/unpacked the source tarball.  Great.
-2.  Type "make all" at the command line.
-3.  If you encountered no errors, then all of the BED Tools should now be in bin/
-	If not, try to troubleshoot then email me: aaronquinlan@gmail.com
-4.  Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
-5.  Use the tools.
-
-
 ===Requests===
 I would be grateful to learn of any problems or suggestions you have for improving these tools.
 

USAGE_EXAMPLES

@@ -10,6 +10,10 @@ http://people.virginia.edu/~arq5x/bedtools.html
 ===Example Usage===  
 
 	intersectBed.  Reports overlaps between features in two BED files.
+	
+	NOTE:  When intersecting SNPs, make sure the coordinate conform to the UCSC format.  That is,
+		   the start position for each SNP should be SNP position - 1 and the end position should
+		   be SNP position.  E.g. chr7	10000001	10000002	rs123464
 		
 			1. Report the base-pair overlap between the features in two BED files.
 			$ intersectBed -a reads.bed -b genes.bed

VERSION

+1.1
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