gunzip -c FDR-01-FIRE-peaks.bed.gz > FDR-01-FIRE-peaks_UCSC.bed

sed -i 's/NC_003070.9/chr1/g' FDR-01-FIRE-peaks_UCSC.bed
sed -i 's/NC_003071.7/chr2/g' FDR-01-FIRE-peaks_UCSC.bed
sed -i 's/NC_003074.8/chr3/g' FDR-01-FIRE-peaks_UCSC.bed
sed -i 's/NC_003075.7/chr4/g' FDR-01-FIRE-peaks_UCSC.bed
sed -i 's/NC_003076.8/chr5/g' FDR-01-FIRE-peaks_UCSC.bed
sed -i 's/NC_000932.1/chrPt/g' FDR-01-FIRE-peaks_UCSC.bed
sed -i 's/NC_037304.1/chrMt/g' FDR-01-FIRE-peaks_UCSC.bed

awk -v OFS="\t" '{if($1 ~ /^chr/) print $1,$2,$3,"id="NR-1,$9}' FDR-01-FIRE-peaks_UCSC.bed > foo
mv foo FDR-01-FIRE-peaks_UCSC.bed
cat "track name=FIRE.peaks.arabidopsis.root_combined" FDR-01-FIRE-peaks_UCSC.bed > FDR-01-FIRE-peaks_arabidopsis_root_UCSC.bed


sed -i 's/NC_003070.9/chr1/g' FDR-FIRE-peaks.bed
sed -i 's/NC_003071.7/chr2/g' FDR-FIRE-peaks.bed
sed -i 's/NC_003074.8/chr3/g' FDR-FIRE-peaks.bed
sed -i 's/NC_003075.7/chr4/g' FDR-FIRE-peaks.bed
sed -i 's/NC_003076.8/chr5/g' FDR-FIRE-peaks.bed
sed -i 's/NC_000932.1/chrPt/g' FDR-FIRE-peaks.bed
sed -i 's/NC_037304.1/chrMt/g' FDR-FIRE-peaks.bed