# Working Directory
cd /dcl01/lieber/ajaffe/Amanda/NucVsCyt

# Open screen and interactive session
qrsh -l mem_free=50G,h_vmem=50G,h_fsize=50G



### Copy over the filtered results files from “/Users/amanda/Dropbox/BrainRNACompartments/intron_retention/IRFinder_GLM.r”

## scripts generated using 
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br1113C1/IRFinder-IR-nondir-cleanIntrons-adultShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br1113C1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br1113N1/IRFinder-IR-nondir-cleanIntrons-adultShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br1113N1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br2046C/IRFinder-IR-nondir-cleanIntrons-adultShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br2046C/  
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br2046N/IRFinder-IR-nondir-cleanIntrons-adultShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br2046N/ 
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br2074C/IRFinder-IR-nondir-cleanIntrons-adultShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br2074C/ 
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br2074N/IRFinder-IR-nondir-cleanIntrons-adultShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br2074N/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5339C1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5339C1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5339N1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5339N1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5340C1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5340C1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5340N1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5340N1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5341C1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5341C1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5341N1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5341N1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br1113C1/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br1113C1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br2046C/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br2046C/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br2074C/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br2074C/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5339C1/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5339C1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5340C1/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5340C1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5341C1/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5341C1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br1113N1/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br1113N1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br2046N/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br2046N/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br2074N/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br2074N/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5339N1/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5339N1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5340N1/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5340N1/
scp ./Dropbox/sorted_figures/IRfinder/PolyA/Br5341N1/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt aprice26@jhpce01.jhsph.edu:/dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/Br5341N1/



module load samtools
cd /dcl01/lieber/ajaffe/Amanda/NucVsCyt/11.29.17/

### Test Adult PolyA Zone differences

/users/aprice26/biotools/IRFinder-1.1.1/bin/analysisWithLowReplicates.pl \
  -A APC_Pooled/IRFinder-IR-nondir-cleanIntrons-adultShared.txt Br1113C1/IRFinder-IR-nondir-cleanIntrons-adultShared.txt Br2046C/IRFinder-IR-nondir-cleanIntrons-adultShared.txt Br2074C/IRFinder-IR-nondir-cleanIntrons-adultShared.txt \
  -B APN_Pooled/IRFinder-IR-nondir-cleanIntrons-adultShared.txt Br1113N1/IRFinder-IR-nondir-cleanIntrons-adultShared.txt Br2046N/IRFinder-IR-nondir-cleanIntrons-adultShared.txt Br2074N/IRFinder-IR-nondir-cleanIntrons-adultShared.txt \
  > Adult_PolyA_Zone_cleanIntrons_adultShared.tab


### Test Fetal PolyA Zone differences

/users/aprice26/biotools/IRFinder-1.1.1/bin/analysisWithLowReplicates.pl \
  -A FPC_Pooled/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt Br5339C1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt Br5340C1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt Br5341C1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt \
  -B FPN_Pooled/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt Br5339N1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt Br5340N1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt Br5341N1/IRFinder-IR-nondir-cleanIntrons-prenatalShared.txt \
  > Fetal_PolyA_Zone_cleanIntrons_prenatalShared.tab 


### Test Nuclear PolyA Age Differences

/users/aprice26/biotools/IRFinder-1.1.1/bin/analysisWithLowReplicates.pl \
  -A APN_Pooled/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt Br1113N1/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt Br2046N/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt Br2074N/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt  \
  -B FPN_Pooled/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt Br5339N1/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt Br5340N1/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt Br5341N1/IRFinder-IR-nondir-cleanIntrons-nucleusShared.txt \
  >  Nuclear_PolyA_Age_cleanIntrons_nucleusShared.tab


### Test Cytosolic PolyA Age Differences

/users/aprice26/biotools/IRFinder-1.1.1/bin/analysisWithLowReplicates.pl \
  -A APC_Pooled/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt Br1113C1/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt Br2046C/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt Br2074C/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt \
  -B FPC_Pooled/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt Br5339C1/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt Br5340C1/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt Br5341C1/IRFinder-IR-nondir-cleanIntrons-cytosolShared.txt \
  >  Cytosol_PolyA_Age_cleanIntrons_cytosolShared.tab
