# FPKM processing RNA-seq
../fpkm.py --experiments ../rna_list.csv -f rna


cut -f10 gencode.v19.annotation_capped_sites.bed | cut -f2 -d ' ' | sort | uniq > protein_coding_genes.txt

# Mapping gene_id to names
cut -f9 gencode.v19.annotation.gtf | grep protein_coding |  cut -f1,5 -d ';' |cut -f2,4 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' >  gencode.v19.annotation_protein_coding_ids.txt

# Graph cutoffs
./cutoff_analysis.py --rpkm gene_matrix/rna.tsv --color '#781F76' --factor RNA --limit 0.4 --protein protein_coding_genes.txt