reczko@max:/data/images/proton/run284/www$ ls ../../run278/*q > samples.txt
reczko@max:/data/images/proton/run284/www$ ls ../../run279/*q >> samples.txt
reczko@max:/data/images/proton/run284/www$ ls ../../run280/*q >> samples.txt
reczko@max:/data/images/proton/run284/www$ ls ../../run281/*q >> samples.txt
awk -f /data/images/proton/make-bam-links-from-fastqID.awk > bam-links1.sh
source bam-links1.sh

grep "reads;" ../../run278/chippip.log > reads.txt
grep "reads;" ../../run279/chippip.log >> reads.txt
grep "reads;" ../../run280/chippip.log >> reads.txt
grep "reads;" ../../run281/chippip.log >> reads.txt

#awk -f /data/images/proton/make-unstranded-sampled-mm10-tracks.awk bam-links1.sh > make-unstranded-sampled-mm10-tracks.sh
awk -v min=10791262 -f /data/images/proton/make-unstranded-sampled-mm10-tracks.awk bam-links1.sh > make-unstranded-sampled-mm10-tracks.sh
chmod u+x make-unstranded-sampled-mm10-tracks.sh
./make-unstranded-sampled-mm10-tracks.sh &> make-unstranded-sampled-mm10-tracks.log &

#@
reczko@max:/data/images/proton/run284/www$ ls ../../run282/*q >> samples2.txt
reczko@max:/data/images/proton/run284/www$ ls ../../run283/*q >> samples2.txt
reczko@max:/data/images/proton/run284/www$ ls ../../run284/*q >> samples2.txt
awk -f /data/images/proton/make-bam-links-from-fastqID2.awk samples2.txt > bam-links2.sh
mv reads.txt reads1.txt
grep "reads;" ../../run282/chippip.log >> reads.txt
grep "reads;" ../../run283/chippip.log >> reads.txt
grep "reads;" ../../run284/chippip.log >> reads.txt


awk -v min=10791262 -f /data/images/proton/make-unstranded-sampled-mm10-tracks.awk bam-links2.sh > make-unstranded-sampled-mm10-tracks2.sh

#@
grep "overall" ../../run278/chippip.log > overall.txt
grep "overall" ../../run279/chippip.log >> overall.txt
grep "overall" ../../run280/chippip.log >> overall.txt
grep "overall" ../../run281/chippip.log >> overall.txt
grep "overall" ../../run282/chippip.log >> overall.txt
grep "overall" ../../run283/chippip.log >> overall.txt
grep "overall" ../../run284/chippip.log >> overall.txt

cat bam-links1.sh bam-links2.sh > bam-links.sh
awk -f /data/images/proton/get-ali-stat1.awk bam-links.sh > ali-stats.txt