# prepare .bed file for genes of interest
reczko@platia:/data/images/proton/run90/pairings/merged_asm_GM$ awk -f /data/results/tools/rnaseq/collect-locus-coords-from-merged-gtf-to-bed.awk merged.gtf > merged.bed

#get bed file for selected genes:
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/cuffdiff2stranded-bed1.awk gene_exp.diff.minlen100.biotype-top100-expressed\ in\ GM-tr-0h.csv > gene_exp.diff.minlen100.biotype-top100-expressed_GM-tr-0h.bed

# expression reduction in top100 0h expressed genes is mostly at 20% to 30% of the genebody
ngs.plot.r -G hg19 -R bed -C 0h_VS_1h_wt_top100.txt -O 0h_VS_1h_wt_top100


# same genes show no real change in SCAN
ngs.plot.r -G hg19 -R bed -C   0h_VS_1h_scan_top100_at_wt.txt -O   0h_VS_1h_scan_top100_at_wt

0h_VS_1h_scan_top100_at_wt.avgprof.pdf


# control: untr_0h_wt vs tr_0h_wt top 100 genes:
reczko@platia:/data/images/proton/run90/pairings/untr_VS_tr_wt/cuffdiff_GM-tr-0h-a_vs_GM-untr-0h-a$ awk -f /data/results/tools/rnaseq/cuffdiff2stranded-bed1.awk gene_exp.diff.minlen100.biotype.top100-GM-untr-0h.csv > gene_exp.diff.minlen100.biotype.top100-GM-untr-0h.bed
ngs.plot.r -G hg19 -R bed -C   untr_vs_tr_wt_top100.txt -O  untr_vs_tr_wt_top100

# control: untr_0h_wt vs untr_0h_scan top 100 genes:
cd /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/cuffdiff2stranded-bed1.awk /data/images/proton/run90/pairings/untr_wt_VS_untr_scan/cuffdiff_GM-untr-0h-a_vs_SCAN-untr-0h-a/gene_exp.diff.minlen100.biotype.sig.top27GM.csv > /data/images/proton/run90/pairings/untr_wt_VS_untr_scan/cuffdiff_GM-untr-0h-a_vs_SCAN-untr-0h-a/gene_exp.diff.minlen100.biotype.sig.top27GM.bed

ngs.plot.r -G hg19 -R bed -C untr_wt_vs_untr_scan_top27.txt -O untr_wt_vs_untr_scan_top27



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/cuffdiff2stranded-bed1.awk gene_exp.diff.minlen100.top100expressedSCAN-tr-0h.csv   > gene_exp.diff.minlen100.biotype-top100-expressed_SCAN-tr-0h.bed

ngs.plot.r -G hg19 -R bed -C 0h_VS_1h_scan_top100.txt -O 0h_VS_1h_scan_top100


ngs.plot.r -G hg19 -R genebody -C 0h_VS_1h_wt_SIG_UP.txt  -O 0h_VS_1h_wt_SIG_UP
ngs.plot.r -G hg19 -R genebody -C 0h_VS_3h_wt_SIG_UP.txt  -O 0h_VS_3h_wt_SIG_UP
ngs.plot.r -G hg19 -R tss -C 0h_VS_1h_wt_SIG_UP.txt  -O 0h_VS_1h_wt_SIG_UP_TSS -L 5000
ngs.plot.r -G hg19 -R tss -C 0h_VS_3h_wt_SIG_UP.txt  -O 0h_VS_3h_wt_SIG_UP_TSS -L 5000


ngs.plot.r -G hg19 -R bed -C 0h_VS_1h_wt_SIG_DOWN.txt  -O 0h_VS_1h_wt_SIG_DOWN




reczko@platia:/data/images/proton/run90/www/ngsplots$ ngs.plot.r -G hg19 -R genebody -C 0h_VS_1h_wt_SIG_DOWN.txt  -O 0h_VS_1h_wt_SIG_DOWN



ngs.plot.r -G hg19 -R genebody -C 0h_VS_1h_scan_shortGenes.txt  -O 0h_VS_1h_scan_shortGenes
ngs.plot.r -G hg19 -R genebody -C 0h_VS_1h_scan_longGenes.txt  -O 0h_VS_1h_scan_longGenes


ngs.plot.r -G hg19 -R genebody -C 0h_VS_1h_wt_shortGenes.txt  -O 0h_VS_1h_wt_shortGenes
ngs.plot.r -G hg19 -R genebody -C 0h_VS_1h_wt_longGenes.txt  -O 0h_VS_1h_wt_longGenes