GSE139815 Processing Pipeline

Publication

Nature methods (2020) — PMID 32393832

Dataset

Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors

1. 1

   MaGeCk was used to process data for lentiCRISPR bulk samples to quantify sgRNA abundances.

   MaGeCk v0.5.9

   $ Bash example

   # Install MaGeCk (if not already installed)
   # conda install -c bioconda mageck
   
   # Define input and output files
   # Replace 'sample.fastq.gz' with your actual lentiCRISPR bulk sample FASTQ file.
   # Replace 'lentiCRISPR_sgRNA_library.txt' with your actual sgRNA library file.
   # The sgRNA library file typically contains sgRNA sequences and their corresponding gene targets.
   INPUT_FASTQ="sample.fastq.gz"
   SGRNA_LIBRARY="lentiCRISPR_sgRNA_library.txt"
   OUTPUT_PREFIX="lentiCRISPR_sgRNA_counts"
   
   # Run MaGeCk to quantify sgRNA abundances
   mageck count -l ${SGRNA_LIBRARY} -n ${OUTPUT_PREFIX} --fastq ${INPUT_FASTQ}

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2. 2

   Targeted microRaft data was processed with CRaftID software (https://github.com/YeoLab/CRaftID)

   CRaftID vnot specified GitHub

   $ Bash example

   # Install CRaftID (if not already installed)
   # CRaftID is a Python script, typically cloned from its repository.
   # git clone https://github.com/YeoLab/CRaftID.git
   # cd CRaftID
   
   # Define input and output paths
   # Replace with actual file paths for your targeted microRaft data, reference genome, and target regions.
   INPUT_FASTQ="targeted_microraft_data.fastq" # Input FASTQ file containing microRaft reads
   OUTPUT_DIR="CRaftID_processed_results" # Directory for CRaftID output
   REFERENCE_FASTA="GRCh38.fasta" # Placeholder for the reference genome FASTA file (e.g., hg38, mm10)
   TARGET_REGIONS_BED="target_regions.bed" # Placeholder for a BED file defining the targeted regions
   
   # Create the output directory if it does not exist
   mkdir -p "${OUTPUT_DIR}"
   
   # Execute CRaftID software
   # Assuming CRaftID.py is in the current working directory or in your system's PATH.
   python CRaftID.py \
       -i "${INPUT_FASTQ}" \
       -o "${OUTPUT_DIR}" \
       -r "${REFERENCE_FASTA}" \
       -t "${TARGET_REGIONS_BED}"

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