This experiment aims to search for CR9114 mutants that can overcome the virus resistance.
- 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.
- ./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
- Input files:
- ./script/CR9114_count_to_freq.py: Converts counts into frequencies.
- Input files: count/count_*.tsv
- Output file: ./data/VariantFreqTable.tsv
- ./script/CR9114_plot_TopClonesFreq.R: Plot the frequencies of top clones in each selection.
- Input file: ./data/VariantFreqTable.tsv
- Output files: graph/Freq_YDisplay_*.png