/data/images/proton/run90/pairings/get-alternative-exons1.sh > get-alternative-exons1.log
@@
reczko@platia:/data/images/proton/run90/pairings/merged_asm$ sort -u merged-events.txt2 > merged-events-uniq.txt2

@@
/data/results/tools/rnaseq/isoforms/README-ASprofile.txt

cd /data/images/proton/run90/pairings/merged_asm/
 cuffcompare -r /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf merged.gtf  

reczko@platia:/data/images/proton/run90/pairings/merged_asm$ /data/results/tools/rnaseq/isoforms/ASprofile.b-1.0.4/extract-as merged.gtf /data/results/tools/rnaseq/isoforms/ASprofile.b-1.0.4/hg19ens.fa.hdrs  > merged-events.txt
reczko@platia:/data/images/proton/run90/pairings/merged_asm$ /data/results/tools/rnaseq/isoforms/ASprofile.b-1.0.4/summarize_as.pl merged.gtf merged-events.txt -p events-summary

reczko@platia:/data/images/proton/run90/pairings/merged_asm$ /data/results/tools/rnaseq/isoforms/ASprofile.b-1.0.4/extract-as merged.gtf /data/results/tools/rnaseq/isoforms/ASprofile.b-1.0.4/hg19ens.fa.hdrs -r /data/images/proton/run90/pairings/merged_asm/cuffcmp.merged.gtf.tmap /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf  > merged-events.txt2

@@
reczko@platia:/data/images/proton/run90/pairings/merged_asm$ /data/results/tools/rnaseq/isoforms/ASprofile.b-1.0.4/extract-as merged.gtf /data/results/tools/rnaseq/isoforms/ASprofile.b-1.0.4/hg19ens.fa.hdrs  > merged-events.txt

reczko@platia:/data/images/proton/run90/pairings/0h_VS_1h_wt/cuffdiff_GM-tr-0h-a_vs_GM-tr-1h-a$ awk -f /data/results/tools/rnaseq/cuffdiff-and-asprofile2stats1.awk gene_exp.diff
133752
condition GM-tr-0h-a
numTSS 20343
numTTS 11073
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 7463

condition GM-tr-1h-a
numTSS 20864
numTTS 11299
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 7656

reczko@platia:/data/images/proton/run90/pairings/0h_VS_3h_wt/cuffdiff_GM-tr-0h-a_vs_GM-tr-3h-a$ awk -f /data/results/tools/rnaseq/cuffdiff-and-asprofile2stats1.awk gene_exp.diff
33752
condition GM-tr-0h-a
numTSS 20702
numTTS 11289
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 7612

condition GM-tr-3h-a
numTSS 21053
numTTS 11497
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 7741

reczko@platia:/data/images/proton/run90/pairings/untr_wt_VS_untr_scan/cuffdiff_GM-untr-0h-a_vs_SCAN-untr-0h-a$ awk -f /data/results/tools/rnaseq/cuffdiff-and-asprofile2stats1.awk gene_exp.diff
33752
condition GM-untr-0h-a
numTSS 48914
numTTS 21001
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 22930

condition SCAN-untr-0h-a
numTSS 51225
numTTS 21802
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 23789

reczko@platia:/data/images/proton/run90/pairings/0h_VS_1h_scan/cuffdiff_SCAN-tr-0h-a_vs_SCAN-tr-1h-a$ awk -f /data/results/tools/rnaseq/cuffdiff-and-asprofile2stats1.awk gene_exp.diff
33752
condition SCAN-tr-0h-a
numTSS 20619
numTTS 11275
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 7305

condition SCAN-tr-1h-a
numTSS 21238
numTTS 11506
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 7491

reczko@platia:/data/images/proton/run90/pairings/0h_VS_3h_scan/cuffdiff_SCAN-tr-0h-a_vs_SCAN-tr-3h-a$ awk -f /data/results/tools/rnaseq/cuffdiff-and-asprofile2stats1.awk gene_exp.diff
33752
condition SCAN-tr-0h-a
numTSS 20848
numTTS 11400
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 7413

condition SCAN-tr-3h-a
numTSS 21340
numTTS 11618
numSKIP_ON 
numSKIP_OFF 
numMSKIP_ON 
numMSKIP_OFF 
numIR_ON 
numIR_OFF 
numMIR_ON 
numMIR_OFF 
numAE 7572