From 1e5b40b411191cf345df9c40d83f91af94d2855e Mon Sep 17 00:00:00 2001 From: Aaron Quinlan <aaronquinlan@gmail.com> Date: Thu, 23 Apr 2009 23:19:18 -0400 Subject: [PATCH] Added VERSION and spruced up USAGE_EXAMPLES --- README | 17 ++++++++--------- USAGE_EXAMPLES | 4 ++++ VERSION | 1 + 3 files changed, 13 insertions(+), 9 deletions(-) create mode 100644 VERSION diff --git a/README b/README index e09fb8d0..62855b3e 100644 --- a/README +++ b/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. diff --git a/USAGE_EXAMPLES b/USAGE_EXAMPLES index 11944394..59fe2fb1 100644 --- a/USAGE_EXAMPLES +++ b/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 diff --git a/VERSION b/VERSION new file mode 100644 index 00000000..b123147e --- /dev/null +++ b/VERSION @@ -0,0 +1 @@ +1.1 \ No newline at end of file -- GitLab