reczko@max:/data/images/proton/ITlab/run299evangelia$  awk -f /data/images/proton/orderTracks.awk SStrackDb.txt > trackDb.txt
reczko@max:/data/images/proton/run299/evangelia/cuffdiff_wt_vs_wtTCP$ Rscript /data/images/proton/cummerbund-report1.r wt wtTCP |tee cummerbund-report.txt
reczko@max:/data/images/proton/ITlab/run299evangelia/cuffdiff_ko_vs_koTCP$ gimp /data/images/proton/run299/evangelia/cuffdiff_wt_vs_wtTCP/wt_vs_wtTCP_known_genes_alpha0.05_with_replicates.png 


cd ../cuffdiff_wt_vs_ko/
Rscript /data/images/proton/cummerbund-report1.r wt ko |tee cummerbund-report.txt
cd ../cuffdiff_ko_vs_koTCP/
Rscript /data/images/proton/cummerbund-report1.r ko koTCP |tee cummerbund-report.txt

cd /data/images/proton/run299/evangelia/cuffdiff_ko_vs_koTCP
Rscript /data/images/proton/cummerbund-report2.r ko koTCP http://genomics-lab.fleming.gr/fleming/ITlab/run299evangelia mm10
cd ../cuffdiff_wtTCP_vs_koTCP$
Rscript /data/images/proton/cummerbund-report2.r wtTCP koTCP http://genomics-lab.fleming.gr/fleming/ITlab/run299evangelia mm10
cd ../cuffdiff_ko_vs_koTCP
Rscript /data/images/proton/cummerbund-report2.r ko koTCP http://genomics-lab.fleming.gr/fleming/ITlab/run299evangelia mm10
cd ../cuffdiff_wt_vs_ko
Rscript /data/images/proton/cummerbund-report2.r wt ko http://genomics-lab.fleming.gr/fleming/ITlab/run299evangelia mm10

#uses ../reads.txt
reczko@max:/mnt/max/c/genomics_facility/proton/run299/evangelia/cuffdiff_wtTCP_vs_koTCP$ Rscript /data/images/proton/cummerbund-report2.r wtTCP koTCP http://genomics-lab.fleming.gr/fleming/ITlab/run299evangelia mm10

ls -l cuf*/*html
-rw-r--r-- 1 reczko users 5958 Jul 19 13:06 cuffdiff_ko_vs_koTCP/cufflinks_report.html
-rw-r--r-- 1 reczko users 5578 Jul 19 13:21 cuffdiff_wtTCP_vs_koTCP/cufflinks_report.html
-rw-r--r-- 1 reczko users 6303 Jul 19 14:18 cuffdiff_wt_vs_ko/cufflinks_report.html