Cottrell_PTRE-seq_scripts

Scripts used in Cottrell et al, 2017 manuscript

Steps and Scripts

1. Library design
   Library was designed manually. This GitHub repo includes the excel file: Library_design.xlsx
   Grouping of regulatory elements into specific categories: Grouped_Barcode_identities.txt

2. Raw sequencing data to Barcode counts
   All replicates were indexed with a different P1 index and pooled and sequenced. FastQ files were first demultiplexed, and then counts were obtained per barcode.
   Script: KC_barcode_counts.sh

3. Preliminary analysis: Counts to RNA expression and TE efficiency
   Script: Analysis_RNA_TE.R
   Files:
        1) RNA_plasmid.txt (RNA Expression)
        2) PARNA_RNA.txt (TE efficiency)
        3) Analysis_cell_type.R (Counts to RNA expression for different cell types)
        4) Analysis_40S.R (Counts to 40S association)

4. Linear Modeling to RNA expression and TE efficiency
   Scripts:
        1) Modeling_linear.R
        2) Exploratory analysis: modeling_FOLD.R
   

5. Scripts for specific data analysis
        1) Analysis of Let7 targets: Let-7_Analysis.R
        2) Analysis of combined effects of Let7 and Pumilio: Pum_Let-7_Analysis.R
        3) Natural target analysis scripts: Natural_Targets_Analysis.R
        4) Analysis of AU-rich element containing reporters: HuR_Analysis
        5) Analysis of reporters with combinations of Let-7 binding sites and AREs: HuR_Let_7_Analysis.R
        6) Analysis of reporters with combinations of PREs and AREs: HuR_Pum_Analysis.R
        7) Analysis of let-7 binding site variants: Seed_PC_Analysis.R