Code for reproducing the analysis of the CRISPR-Cas9 genome-wide screen in HeLa cells
To reproduce the complete analysis you just need to execute the provided R markdown file after putting the raw FASTQ files (accessible from GEO) under the following directories:
- data/original_data/lib1/ (for FASTQ files of TKOv1 library 1)
- data/original_data/lib2/ (for FASTQ files of TKOv1 library 2)
FASTQ files that belong to library 1: Moffat_3_CGCTCATT-CCTATCCT_L001_R1_001.fastq.gz, Moffat_5_ATTACTCG-TATAGCCT_L002_R1_001.fastq.gz, Moffat_6_TCCGGAGA-TATAGCCT_L002_R1_001.fastq.gz, Moffat_7_CGCTCATT-TATAGCCT_L002_R1_001.fastq.gz, Moffat_53_ATTACTCG-TATAGCCT_L006_R1_001.fastq.gz, Moffat_54_TCCGGAGA-TATAGCCT_L006_R1_001.fastq.gz and Moffat_55_CGCTCATT-TATAGCCT_L006_R1_001.fastq.gz.
FASTQ files that belong to library 2: Moffat_4_GAGATTCC-GGCTCTGA_L001_R1_001.fastq.gz, Moffat_17_ATTACTCG-TATAGCCT_L003_R1_001.fastq.gz, Moffat_18_TCCGGAGA-TATAGCCT_L003_R1_001.fastq.gz, Moffat_19_CGCTCATT-TATAGCCT_L003_R1_001.fastq.gz, Moffat_62_TCCGGAGA-TAATCTTA_L006_R1_001.fastq.gz, Moffat_63_CGCTCATT-TAATCTTA_L006_R1_001.fastq.gz and Moffat_64_GAGATTCC-TAATCTTA_L006_R1_001.fastq.gz