/CR9114mut

Primary LanguagePython

ANALYSIS FOR CR9114 DEEP MUTATIONAL SCANNING

This experiment aims to search for CR9114 mutants that can overcome the virus resistance.

INPUT FILE

  • All raw sequencing reads, which can be downloaded from NIH SRA database PRJNA510700, should be placed in fastq/ folder. The filename for read 1 should match those described in ./doc/SampleID.tsv. The filename for read 2 should be the same as read 1 except "R1" is replaced by "R2".
  • ./doc/SampleID.tsv: Describes the sample identity for each fastq file.

ANALYSIS PIPELINE

  1. ./script/CR9114_read_to_count.py: Converts raw reads to variant counts.
    • Input files:
      • Raw sequencing reads in fastq/ folder
    • Output files: count/count_*.tsv
  2. ./script/CR9114_count_to_freq.py: Converts counts into frequencies.

PLOTTING

  1. ./script/CR9114_plot_TopClonesFreq.R: Plot the frequencies of top clones in each selection.