# On server 4,

< /media/DATA/Amanda/fullnames.txt parallel -P23 read_distribution.py -i /media/DATA/Amanda/NucVSCyt/{}_accepted_hits.sorted.bam -r /home/nina/rseqc_data/hg19.RefSeq_gene.bed ">" /media/DATA/Amanda/read_distribution/{}.dist.txt
read_distribution.py -i /media/DATA/Amanda/NucVSCyt/Br5340C1_downsamp_accepted_hits.sorted.bam -r /home/nina/rseqc_data/hg19.RefSeq_gene.bed > /media/DATA/Amanda/read_distribution/Br5340C1_downsamp.dist.txt
read_distribution.py -i /media/DATA/Amanda/NucVSCyt/Br5339C1_downsamp_accepted_hits.sorted.bam -r /home/nina/rseqc_data/hg19.RefSeq_gene.bed > /media/DATA/Amanda/read_distribution/Br5339C1_downsamp.dist.txt

# On biostat cluster,

scp amanda@10.17.9.91:/media/DATA/Amanda/read_distribution/*.dist.txt /dcl01/lieber/ajaffe/Amanda/NucVsCyt/read_distribution/

# continue analysis using /Users/amanda/Dropbox/BrainRNACompartments/characterize_fractioned_transcriptome/read_distribution.R 
