#!/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