reczko@platia:/data/images/proton/run268$ bamToFastq -i /data/images/proton/run268/IonXpressRNA_015_rawlib.basecaller.bam -fq R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_015.fq
reczko@platia:/data/images/proton/run268$ /data/results/tools/align/bowtie2-2.2.3/bowtie2 -x /data/images/proton/run149/bb_wo_ins R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_015.fq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_015.bam

GSkP4-Ab42Lib  (IonXpressRNA_015.bam)
3966886 reads; of these:
  3966886 (100.00%) were unpaired; of these:
    1710610 (43.12%) aligned 0 times
    2256276 (56.88%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
56.88% overall alignment rate

GSkP5_SOD-Lib (IonXpressRNA_016.bam)
5138815 reads; of these:
  5138815 (100.00%) were unpaired; of these:
    404728 (7.88%) aligned 0 times
    4734087 (92.12%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
92.12% overall alignment rate



bamToFastq -i /data/images/proton/run268/IonXpressRNA_016_rawlib.basecaller.bam -fq R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_016.fq

/data/results/tools/align/bowtie2-2.2.3/bowtie2 -x /data/images/proton/run149/bb_wo_ins R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_016.fq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_016.bam

cd t
samtools view  ../R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_015.bam |split -99999

../get-ins2.sh
for i in *ins
 do
 cat $i >> ins.fa
 done
mv ins.fa ../GSkP4-Ab42Lib.IonXpressRNA_015.ins.fa
samtools view  ../R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_016.bam |split -99999
../get-ins2.sh

cd ..
/data/results/tools/align/multiple/cd-hit-v4.6.1-2012-08-27/cd-hit-est -i  GSkP4-Ab42Lib.IonXpressRNA_015.ins.fa -o  GSkP4-Ab42Lib.IonXpressRNA_015.ins.fa.clust -c 0.95 -n 5    -S 0 -r 0 -M 40000 &>  GSkP4-Ab42Lib.IonXpressRNA_015.ins.fa.log

cd ..
/data/results/tools/align/multiple/cd-hit-v4.6.1-2012-08-27/cd-hit-est -i  GSkP4-Ab42Lib.IonXpressRNA_016.ins.fa -o  GSkP4-Ab42Lib.IonXpressRNA_016.ins.fa.clust -c 0.95 -n 5    -S 0 -r 0 -M 40000 &>  GSkP4-Ab42Lib.IonXpressRNA_016.ins.fa.log

reczko@platia:/data/images/proton/run268$ echo "GSkP4-Ab42Lib.IonXpressRNA_015.ins.fa.clust" |   awk -f /data/results/tools/align/multiple/cd-hit-clust-sizes1.awk  
read GSkP4-Ab42Lib.IonXpressRNA_015.ins.fa.clust
nread 85397     VAQJ1:03985:08902 1
reczko@platia:/data/images/proton/run268$ echo "GSkP4-Ab42Lib.IonXpressRNA_016.ins.fa.clust" |   awk -f /data/results/tools/align/multiple/cd-hit-clust-sizes1.awk  
read GSkP4-Ab42Lib.IonXpressRNA_016.ins.fa.clust
nread 17643     VAQJ1:03974:08721 1

ls *.clstr.size.fa  > insert_samples.txt
awk -f  merge-inserts2.awk  insert_samples.txt > insert_samples.csv


#@@ 29022016
reczko@estia:/data/images/proton/run149$ awk -f  /data/images/proton/run149/count-exclusive1.awk insert_samples.csv
4407514 1 5 16
reczko@estia:/data/images/proton/run149$ awk -f  /data/images/proton/run149/get-exclusive1.awk insert_samples.csv
4407514 1 5 16
IMP1 1459 AGCGGCGGCACCGGGCGC
IMP2 1483 ACCGCCTCCTGGTGG
IMP2 1277 ACCGCCGAGCTTCGTGG
IMP2 1073 ACCTCGAGCGTTCTGG
IMP2 1017 ACCGGCTCGTGTGG
IMP2 1016 AGCGGCATCAGCAGCTGG
IMP3 1030 TGCGCGAGGTGCGG
IMP3 1037 ACCACCGAGCGCCCGC
IMP3 1416 ACCACCTGGTCGCGG
IMP3 1428 ACCCCGACCACGGTCCTG
IMP3 1058 TGCATGGTCGTCTTC
IMP3 1077 GCGCCGAGGTGCGG
IMP3 1708 TGCGTCATCGTGCGGACG
IMP3 1507 TGCTGCATCGCGTTC
IMP3 1358 CACCCCCGGCCCTGGTTCGAC
IMP3 1256 TCGCACGGTGATGATC
IMP3 1667 ACGCGAACGTGAGG
IMP3 1012 TGCACGATCCACCGG
IMP3 1550 AGCAGCTGGGCGCGG
IMP3 1001 ACCACCTGGACGGTC
IMP3 1126 ACCACGGTGACGATC
IMP3 1521 CACCACGTCACGCCAGG

reczko@estia:/data/images/proton/run149$ awk -f  /data/images/proton/run149/get-avg-insert-len.awk insert_samples.csv
4407514 20.609
4^21=
4398046511104

3 start-codons
6 S positions
12 N positions
=3 * 2^6 * 4^12
=3*24*16777216
=2147483648