Thursday, April 24, 2014

Tutorial Bedtools Bedtool


#!/bin/sh

##### PARAMTER for INTERSECT######:
## mention strandness
# -s
# print A , with number of Hit
#  -c
# print A , with number of bp overlap
# -wo



##### EXAMPLE ####
f1="coding.withrpt.bed.tmp"
f2="noncoding.withrpt.bed.tmp"
f1Out="coding.withrpt.bed"
f2Out="noncoding.withrpt.bed"

fCDS="refseqcoding.CDS.bed"

# bedtools intersect -s -c  -a $f1 -b $fCDS  > $f1Out
# bedtools intersect -s -wo  -a $f1 -b $fCDS  > $f1Out.bp

# bedtools intersect -s -c  -a $f2 -b $fCDS  > $f2Out
# bedtools intersect -s -wo  -a $f2 -b $fCDS  > $f2Out.bp

# bedtools intersect -s -wo -a test1.bed -b test2.bed



##### PARAMTER for GETFASTA ######:
## mention strandness
# -s
## input and output file
# -fi  -fo

##### EXAMPLE ####
fAllgeneBed="allGene.bed"
fAllgeneFasta="allGene.fasta"
# bedtools getfasta  -s  -fi /home/data/genomes/hg19/hg19.fa -bed $fAllgeneBed -fo $fAllgeneFasta