for fl in wgEncode*.broadPeak; do /afs/ir/class/cs273a/bin/overlapSelect -selectCoordCols=0,1,2 -inCoordCols=0,1,2 hg19.knownGene.codingExons.bed ${fl} “${fl}_observed_overlaps_coding.bed”; done
for fl in wgEncode*.broadPeak; do /afs/ir/class/cs273a/bin/overlapSelect -selectCoordCols=0,1,2 -inCoordCols=0,1,2 wgEncodeAwgDnaseDukeOsteoblUniPk.narrowPeak ${fl} “${fl}_observed_overlaps_narrow.bed”; done
for hist in H3k27me3Pk blH3k36me3StdPk blH3k27acStdPk; do
for i in $(seq 100); do
/afs/ir/class/cs273a/bin/overlapSelect -selectCoordCols=0,1,2 -inCoordCols=0,1,2 hg19.knownGene.codingExons.bed “wgEncodeBroadHistoneOsteo${hist}.broadPeak_shuffle_${i}.bed” “${hist}_shuffle_${i}_coding_overlap.bed”;
/afs/ir/class/cs273a/bin/overlapSelect -selectCoordCols=0,1,2 -inCoordCols=0,1,2 wgEncodeAwgDnaseDukeOsteoblUniPk.narrowPeak “wgEncodeBroadHistoneOsteo${hist}.broadPeak_shuffle_${i}.bed” “${hist}_shuffle_${i}_narrow_overlap.bed”;
done;
done