cd /data/images/proton2/run379/www
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
cd ../../run380/www
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

cd /data/images/proton2/run355/www/merged2/
awk -f /data/images/proton2/make-unstranded-sampled-mm10-tracks2.awk  reads.txt-g1  > make-unstranded-sampled-mm10-tracks.sh
#Sampling to smallest library containing13836571 reads
source make-unstranded-sampled-mm10-tracks.sh
mv hub.txt hub-g1.txt	    
mv genomes.txt genomes-g1.txt   
mv StrackDb.txt StrackDb-g1.txt 

awk -f /data/images/proton2/make-unstranded-sampled-mm10-tracks2.awk  reads.txt-g2  > make-unstranded-sampled-mm10-tracks.sh
#Sampling to smallest library containing11117713 reads
source make-unstranded-sampled-mm10-tracks.sh
mv hub.txt hub-g2.txt	    
mv genomes.txt genomes-g2.txt   
mv StrackDb.txt StrackDb-g2.txt 

awk -f /data/images/proton2/make-unstranded-sampled-mm10-tracks2.awk  reads.txt-g3  > make-unstranded-sampled-mm10-tracks.sh
#Sampling to smallest library containing20768721 reads
source make-unstranded-sampled-mm10-tracks.sh
mv hub.txt hub-g3.txt	    
mv genomes.txt genomes-g3.txt   
mv StrackDb.txt StrackDb-g3.txt 

cd /data/images/proton2/run357/www/merged
awk -f /data/images/proton2/make-unstranded-sampled-mm10-tracks2.awk  reads.txt-g4  > make-unstranded-sampled-mm10-tracks.sh
#Sampling to smallest library containing15196514 reads
source make-unstranded-sampled-mm10-tracks.sh
mv hub.txt hub-g4.txt	    
mv genomes.txt genomes-g4.txt   
mv StrackDb.txt StrackDb-g4.txt 

cd /data/images/proton2/run358/www/merged
awk -f /data/images/proton2/make-unstranded-sampled-mm10-tracks2.awk  reads.txt-g5  > make-unstranded-sampled-mm10-tracks.sh
#Sampling to smallest library containing13036786 reads
source make-unstranded-sampled-mm10-tracks.sh
mv hub.txt hub-g5.txt	    
mv genomes.txt genomes-g5.txt   
mv StrackDb.txt StrackDb-g5.txt 

awk -f /data/images/proton2/make-unstranded-sampled-mm10-tracks2.awk  reads.txt-g6  > make-unstranded-sampled-mm10-tracks.sh
#Sampling to smallest library containing13388721 reads
source make-unstranded-sampled-mm10-tracks.sh
mv hub.txt hub-g6.txt	    
mv genomes.txt genomes-g6.txt   
mv StrackDb.txt StrackDb-g6.txt 

cd /data/images/proton2/ITlba
ln -s /data/images/proton2/run358/www/merged run358m
ln -s /data/images/proton2/run357/www/merged run357m
ln -s /data/images/proton2/run355/www/merged2 run355m

Dear Iannis,

the alignments and normalizations as specified in the document "Talianidis-Seq analysis.docx"
are ready.
The track hubs are named g1 to g6 according to the 6 sections in that document.
For each hub, the libraries and the number of mapped reads are also specified.

http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/ITlab/run355m/hub-g1.txt
Sampled to smallest library containing 13836571 mapped reads
ITRC27-BrEU-wt3  13836571
ITRC28-BrEU-wt4  22947817

http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/ITlab/run355m/hub-g2.txt
Sampled to smallest library containing 11117713 mapped reads
ITRC29-GRO-DENTC-wt1a       11117713
ITRC30-GRO-DENTC-wt1b       16764268
ITRC31-GRO-USP22-DENTC-ko1  22113864
ITRC32-GRO-USP22-DENTC-ko2  18104063
ITRC33-GRO-USP22-DENTC-ko3  27592020

http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/ITlab/run355m/hub-g3.txt
Sampled to smallest library containing 20768721 mapped reads
ITRC34-EU-wt1              26618633
ITRC35-EU-wt2              31841013
ITRC36-EU-USP22-ko1        26918704
ITRC37-EU-USP22-ko2        25540542
ITRC38-EU-DENTC-wt2        39315744
ITRC39-EU-DENTC-wt3        32865580
ITRC40-EU-USP22-DENTC-ko4  33492260
ITRC41-EU-USP22-DENTC-ko5  20768721

http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/ITlab/run357m/hub-g4.txt
Sampled to smallest library containing 15196514 mapped reads
ITC274-PolII-wt3       24439033
ITC275-PolII-wt4       24928388
ITC276-PolII-DENwt1    21251881
ITC277-PolII-DENwt2    22254115
ITC278-PolII-AlSm1     18990338
ITC279-PolII-AlSm2     15919784
ITC280-PolII-DENAlSm3  16906098
ITC281-PolII-DENAlSm4  15196514

http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/ITlab/run358m/hub-g5.txt
Sampled to smallest library containing 13036786 mapped reads
ITC290-Pho-wt3       35249319
ITC293-Pho-DENwt2    34175026
ITC294-Pho-AlSm1     16835267
ITC295-Pho-AlSm2     13036786
ITC296-Pho-DENAlSm3  20548604
ITC297-Pho-DENAlSm4  16518765

http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/ITlab/run358m/hub-g6.txt
Sampled to smallest library containing 13388721 mapped reads
ITC298-PolII-Untrwt3    19699666
ITC299-PolII-Untrwt4    28757732
ITC300-PolII-Untrko1    18736870
ITC301-PolII-Untrko3    13388721
ITC302-PolII-DENTCPwt1  21164943
ITC303-PolII-DENTCPwt3  16287734
ITC304-PolII-DENTCPko2  20323907
ITC305-PolII-DENTCPko4  25194941


Best wishes,
Martin