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Cas13a guide design

Data needed

  • reference genome sequence (.fa)
  • sequenced viral genomes representing genetic diversity (.fa)
  • Cas13a repeat sequence

Need to install:

  • bowtie
  • RNAfold
  • R, with libraries: optparse, here, Biostrings, parallel, doParallel

Workflow (using scripts)

Documentation

  1. Break reference genome into windows of 20nt: break_genome.R
  • need reference genome .fa file
  1. Score window sensitivity to SARS-CoV-2: score_SARS-CoV-2_sensitivity.R
  • need .fa file of sequenced viral genomes representing genetic diversity
  1. Score specificity against other human coronaviruses: score_human_CoV_specificity.R
  • need .fa file of offtarget coronavirus genomes

  1. Calculate crRNA folding structures (RNAfold): score_RNAfold_crRNAs.R

  2. Calculate base-pairing propensity of viral target window: score_RNAfold_target.R

  3. Align against hg38 transcriptome: align_bowtie.R

  4. Align against bosTau9 transcriptome: align_bowtie.R

  5. Compile scores into aggregate summary table: compile_scores.R

sample processing script: outputs/covid/cas13a_20nt/process.sh