reczko@fix:/data/images/proton2/run404$ ../chipSeq-pip-dm6.sh
reczko@fix:/data/images/proton2/run404$ ./chippip.sh &> chippip.log &
cd /data/images/proton2/run404/DrVerrijzer/
awk -v p="`pwd`" -f /data/images/proton/link-chipseq-bam-files-to-sample-ids2.awk ../samples.txt > make-links.sh
source make-links.sh

awk -f /data/images/proton/make-unstranded-dmel-tracks1.awk  reads.txt  > make-unstranded-dmel-tracks.sh
awk -f /data/images/proton2/make-unstranded-sampled-dme-tracks.awk  reads.txt  > make-unstranded-sampled-dme-tracks.sh
run393:
/data/images/proton/external/DrVerrijzer/run393/PVC1-GFPBrm1.bam
/data/images/proton/external/DrVerrijzer/run393/PVC2-GFPBrm2.bam
/data/images/proton/external/DrVerrijzer/run393/PVC3-GFPK804R1.bam
/data/images/proton/external/DrVerrijzer/run393/PVC4-GFPK804R2.bam
/data/images/proton/external/DrVerrijzer/run393/PVC5-S2mock1.bam
/data/images/proton/external/DrVerrijzer/run393/PVC6-S2mock2.bam
/data/images/proton/external/DrVerrijzer/run393/PVC7-InputBrm.bam 

run404:
PVC1-GFPBrm1.bam
PVC2-GFPBrm2.bam
PVC3-GFPK804R1.bam
PVC4-GFPK804R2.bam
PVC5-S2mock1.bam
PVC6-S2mock2.bam
PVC7-InputBrm.bam

awk -f /data/images/proton/make-unstranded-sampled-mm9-tracks-merging-pairs1.awk reads.txt
sortedwt01pos.sorted.bam 78892142
sortedwt02pos.sorted.bam 80142586
sortedwt21pos.bam 74306938
sortedwt22pos.bam 87248728


samtools merge PVC1-GFPBrm1.m.bam PVC1-GFPBrm1.bam     /data/images/proton/external/DrVerrijzer/run393/PVC1-GFPBrm1.bam  
samtools merge PVC2-GFPBrm2.m.bam PVC2-GFPBrm2.bam     /data/images/proton/external/DrVerrijzer/run393/PVC2-GFPBrm2.bam  
samtools merge PVC3-GFPK804R1.m.bam PVC3-GFPK804R1.bam   /data/images/proton/external/DrVerrijzer/run393/PVC3-GFPK804R1.bam
samtools merge PVC4-GFPK804R2.m.bam PVC4-GFPK804R2.bam   /data/images/proton/external/DrVerrijzer/run393/PVC4-GFPK804R2.bam
samtools merge PVC5-S2mock1.m.bam PVC5-S2mock1.bam     /data/images/proton/external/DrVerrijzer/run393/PVC5-S2mock1.bam  
samtools merge PVC6-S2mock2.m.bam PVC6-S2mock2.bam     /data/images/proton/external/DrVerrijzer/run393/PVC6-S2mock2.bam  
samtools merge PVC7-InputBrm.m.bam PVC7-InputBrm.bam    /data/images/proton/external/DrVerrijzer/run393/PVC7-InputBrm.bam 

awk -f /data/images/proton/make-unstranded-dmel-tracks1.awk  reads.m.txt  > make-unstranded-dmel-tracks.sh

# merge replicates
samtools merge PVC1-GFPBrm1.m2.bam PVC1-GFPBrm1.m.bam PVC2-GFPBrm2.m.bam
samtools merge PVC3-GFPK804R1.m2.bam PVC3-GFPK804R1.m.bam PVC4-GFPK804R2.m.bam
samtools merge PVC5-S2mock1.m2.bam PVC5-S2mock1.m.bam PVC6-S2mock2.m.bam