ls -d HS* | xargs -i echo "cd {}; cat \$(find . -regex '.*tophat_wj/junctions.bed' | tr '\n' ' ') > all_juncts.bed; cd .. " | bash
find . -name .snapshot -prune -o -name all_juncts.bed | grep -v snapshot | xargs -i echo "cat {} | sed 's/,/ /g' | shrinkwrap | awk '{ print \$1, \$2+\$13+1, \$2+\$NF,\$4, \$5}' > {}.introns" | bash
find . -name .snapshot -prune -o -name all_juncts.bed.introns | grep -v snapshot | xargs -i echo "/home/rcorbett/slx_service_rc/trunk/merge_introns.py -i {} | sort +0 -3 > {}.merged " | bash
find . -name .snapshot -prune -o -name all_juncts.bed.introns.merged | grep -v snapshot | xargs -i echo "/home/rchiu/work/wtss/mouse/corbett/compare_introns.pl /projects/NBL//reference_files/UCSC/all.gff.introns.txt.unique {} {}.ref {}.nov" | bash