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Scripts and misc. for the paper:

Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes from natural populations

This project was funded by the Univeristy of California, Irvine Malaria Inititive

NOTE: Large datafiles (eg. vcf files) will gladly be provided upon request.

  • sample_meta.xlsx : sample lists and metadata for the VGL (Vector Genetics Lab) samples used in this study
  • notes.md : working notes for running chopchop on all transcripts from a genome
  • all_transcript_runs/ : scripts and log files from running chopchop on all transcripts for AgamP4.11 and AaegL5.1
  • utils/ : additional small scripts used in preparing datafiles for chopchop
  • parsing/ : iPython notebooks used to process all_transcript_runs results
  • variants/ : iPython notebooks used to process variant data, collate it with all_transcript_runs, and produce statistics and figures