synonymous-citrines/run.sh at main · lareaulab/synonymous-citrines · GitHub

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#!/bin/sh

######
# figure 1: new data on wildtype reporters, newly constructed for this paper based on Tunney et al
######

# codon speeds of each construct
R CMD BATCH figure_code/citrine_speeds_tunney_figure.R

# construct scores relative to endogenous genes
R CMD BATCH figure_code/endogenous_histogram.R

# (the flow and qPCR data are from the same run as figure 6, stemloop)

# flow of citrine constructs
R CMD BATCH analysis_code/stemloop/stemloop_protein_normgate.R
R CMD BATCH figure_code/WT/EFL_protein_plot.R

# qPCR of citrine constructs
R CMD BATCH analysis_code/stemloop/SL_mRNA_deltaCq.R
R CMD BATCH figure_code/WT/EFL_mRNA_plot.R

# TE of citrine constructs
R CMD BATCH figure_code/WT/EFL_TE_plot.R


######
# figure 2: TASEP model and polysome profiles
######

# TASEP (also makes two supp. figures)
R CMD BATCH figure_code/tasep_plots.R

# polysome gradients
R CMD BATCH figure_code/polysome_plots.R

######
# figure 3: RQC knockouts and E2A reporter
######

# RQC knockouts
# (the knockouts and chimeras are in the same flow run - process the data for both)
R CMD BATCH analysis_code/knockouts_chimeras_analysis.R
R CMD BATCH figure_code/knockouts_plot.R

# 2A reporter construct
R CMD BATCH analysis_code/E2A_normgate.R
R CMD BATCH figure_code/E2A_plot.R

######
# figure 4: start codon occlusion
######

# TASEP occlusion plot generated by the same script as above:
# R CMD BATCH figure_code/tasep_plots.R

# 5' standardized constructs
R CMD BATCH analysis_code/5pstandardized_flow_processing_normgate.R
R CMD BATCH figure_code/5prime_standardized_plot.R

# chimera constructs
# (chimera data was analyzed in the same flow run as RQC knockouts, above)
R CMD BATCH figure_code/chimera_plot.R

######
# figure 5: CRISPRi
######

# main ciber-seq results
R CMD BATCH figure_code/ciber-seq_plot.R

# individual crispri confirmations (protein)
R CMD BATCH analysis_code/individual_CRISPRi/crispri_protein_normgate.R
R CMD BATCH figure_code/individual_CRISPRi/crispri_protein_plot.R


######
# figure 6: stem loops
######

# the data are from the same run as figure 1
R CMD BATCH figure_code/stemloop_figures.R


#######################
# supp figures
#######################

######
# supp figures: CRISPRi and CiBER-seq controls
######

# ZEM fusion fluorescence
R CMD BATCH analysis_code/CiBER-seq/ZEM-cit_control_protein_normgate.R
R CMD BATCH figure_code/CiBERseq/ZEM-cit_control_plot.R

# CRISPRi growth defect controls
R CMD BATCH analysis_code/individual_CRISPRi/crispri_growthdefectscontrols_protein_normgate.R
R CMD BATCH figure_code/individual_CRISPRi/crispri_growthdefectcontrols_plot.R

# individual crispri confirmations (mRNA + protein)
R CMD BATCH analysis_code/individual_CRISPRi/crispri_te_with_errorprop.R
R CMD BATCH figure_code/individual_CRISPRi/crispri_te_plot.R