###writing how I curated macs files to upload to genome browser


#1)  narrow or broad files to bed files with few columns

extract_columns_que.sh

awk '{print $1,$2,$3}' BRG-me3_binucleosome-SBV5-cntrl_peaks.broadPeak > BRG-me3_binucleosome-SBV5-cntrl_peaks.bed &


#2) sort bed files
==> bedsort.sh <==
for i in *peaks.bed;
do echo " LC_COLLATE=C sort -k1,1 -k2,2n $i > ${i%*.bed}_sorted.bed &"; done > bedsort_que.sh


#3) To change column 4 value to max of 1000 (if its >1000 it gives error)


==> bedsort_score.sh <==

for i in *_sorted.bed;
do (cat $i | perl -p -e 'chomp;@v=split(/\t/);if ($v[4] > 1000){$v[4] = 1000;}$line=join("\t",@v);$_="$line\n";' > ${i%*_sorted.bed}_sorted1.bed); done

##4) bedto bigbed

bedToBigBed BRG-me3_binucleosome-SBme3-cntrl_peaks_sorted.bed ~/reference_genome/hg19/hg19.chromSizes BRG-me3_binucleosome-SBme3-cntrl_peaks.bb