./chipcor -A "DNaseI-HS +" -B "DNaseI-HS -" -b-1000 -e1000 -w 10 </data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelUt189AlnRep2V2.sga

./chipcor -A "DNaseI-HS +" -B "DNaseI-HS -" -b-1000 -e1000 -w 10 /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelUt189AlnRep2V2.sga

time ./chipcor -A "DNaseI-HS +" -B "DNaseI-HS -" -b-1000 -e1000 -w 10 </data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga

time ./chipcor -A "DNaseI-HS +" -B "DNaseI-HS -" -b-1000 -e1000 -w 10 /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga

less /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga | ./chipcor -A "DNaseI-HS +" -B "DNaseI-HS -" -b-1000 -e1000 -w 10

less /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga | ./chipcor -A "DNaseI-HS +" -B "DNaseI-HS -" -b-1000 -e1000 -w 10 -

time ./chippeak -f "DNaseI-HS -" -w 200 -v 200 < /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga

time ./chippeak -f "DNaseI-HS -" -w 200 -v 200 /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga

time ./chippeak -f "DNaseI-HS -" -w 200 -v 200 < /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga > chippeak.t1

time chippeak -f "DNaseI-HS -" -w 200 -v 200 /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga > chippeak.t2

less /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga | ./chippeak -f "DNaseI-HS -" -w 200 -v 200 -

time ./chippart -f "DNaseI-HS" -s0.06 -p-10 /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga

time ./chippart -f "DNaseI-HS" -s0.06 -p-10 < /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga

less /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelUt189AlnRep2V2.sga | ./chippart -d -f "DNaseI-HS" -s0.06 -p-10 -

less /data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelUt189AlnRep2V2.sga | ./chippart -d -f "DNaseI-HS" -s0.06 -p-10


time ./chipcenter -f "DNaseI-HS" -s 70 </data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga > centered.sga


time ./chipscore -A "DNaseI-HS +" -B "DNaseI-HS -" -b-100 -e100 -t 200 </data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga

time ./chipcenter -s 70 </data/mga/hg19/encode/Duke-DNaseI-HS/wgEncodeOpenChromDnaseUrothelAlnRep2V2.sga > centered.sga

chipcenter -s 75 /export/data/mga/hg19/robertson07/STAT1_stim.sga > STAT1_stim_cent_old.sga

./chipcenter -s 75 /export/data/mga/hg19/robertson07/STAT1_stim.sga > STAT1_stim_cent.sga

diff STAT1_stim_cent_old.sga STAT1_stim_cent.sga  OK !!
