script='/data/zhang/makerman/SOLEXA/bedToBrowser/SCRIPT'
path=$PWD
for file in C.nonrund.bed E.nonrund.bed
do
#echo "invert $file control"
#perl $script/invert.errors.in.bed.file.pl $file > $file.fix1.bed
#echo "remove $file control"
#perl $script/remove.errors.in.bed.file.pl  $file> $file.fix2.bed
#echo "sort $file"
#sort -k1,1 -k2,2n < $file.fix2.bed > $file.fix2.sort.bed
#echo "partition control"
#perl $script/Partition.bed.exn.jnc.pl $file.fix2.sort.bed
#echo "make bedgraph $file exn
#sh bedgraph.BATCH.sh $file.fix2.sort.bed.exn.bed
#echo "make bedgraph $file jnc
#sh bedgraph.BATCH.sh $file.fix2.sort.bed.jnc.bed
#make bigWig $file exn
#qsub -e $PWD -o $PWD bw.sh $path/$file.fix2.sort.bed.exn.bed.bedgraph
#make bigWig $file jnc
#qsub -e $PWD -o $PWD bw.sh $path/$file.fix2.sort.bed.jnc.bed.bedgraph 

done

#rm bw.sh.e*
#rm bw.sh.o*