HOW TO INSTALL BEDTOOLS
-----------------------
google "bedtools"
click on code.google.com/p/bedtools
	... bedtools.readthedocs.org
	... sourceforge.net
	... github.com
scp B<TAB> workshop@192.168.56.101:src
	... CyberDuck 
ssh workshop@192.168.56.101
cd src
tar xzvf B<TAB>
cd be<TAB>
less REA<TAB>
make
ls bin
/home/workshop/src/bedtools-2.17.0/bin/bedtools
echo $PATH
cp bin/* ~/bin
bedtools


EXAMPLE 1: INTERSECTBED
-----------------------
intersect cartoon at readthedocs.org

google "bed format"
click on genome.ucsc.edu
	... broadinstitute.org
chrom chromStart chromEnd [name ...]
cd ~/autism
nano interesting.bed
	PTEN	1000	2000	exon1
	PTEN	60000	70000	exon2

intersectBed -abam sample2_sorted.bam -b interesting.bed | samtools view - | less -S


EXAMPLE 2: CLOSESTBED
---------------------
bamToBed <CTRL>-C
bamToBed -?
bamToBed -i sample2_sorted.bam | head
bamToBed -i sample2_sorted.bam | closestBed -a - -b interesting.bed | less
/PTEN


EXAMPLE 3: AUDIENCE REQUEST
---------------------------
???
maskfasta cartoon at readthedocs.org

bamToBed -i sample2_sorted.bam | maskFastaFromBed -fi ~/genomes/autism101.fa -fo autism101-masked.fa -bed -


HOW TO GET ANNOTATION FILES
---------------------------
UCSC TableBrowser
Ensembl
iGenomes