GSE137258 Processing Pipeline

Publication

Molecular cell (2021) — PMID 34216543

Dataset

Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer

1. 1

   Library strategy: DNA-seq

   FastQC (Inferred with models/gemini-2.5-flash) v0.11.9 (Inferred with models/gemini-2.5-flash) GitHub

   $ Bash example

   # Install FastQC (if not already installed)
   # conda install -c bioconda fastqc
   
   # Define input FASTQ files and output directory
   # Replace with actual paths to your DNA-seq raw data
   READ1="sample_R1.fastq.gz"
   READ2="sample_R2.fastq.gz"
   OUTPUT_DIR="fastqc_results"
   
   # Create output directory if it doesn't exist
   mkdir -p "${OUTPUT_DIR}"
   
   # Run FastQC on the raw DNA-seq FASTQ files
   # This performs quality control checks on the sequencing data
   fastqc "${READ1}" "${READ2}" -o "${OUTPUT_DIR}"

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2. 2

   CRISPR screening data was aligned and processed using MaGeCK.

   MaGeCK v0.5.9.3

   $ Bash example

   # Install MaGeCK (if not already installed)
   # conda install -c bioconda mageck
   
   # Example: Perform MaGeCK analysis for gene essentiality testing.
   # This assumes 'sgRNA_counts.txt' contains read counts for sgRNAs across samples,
   # 'sgRNA_library.txt' maps sgRNAs to target genes, and 'design_matrix.txt'
   # specifies control and treatment samples. Replace placeholder file names and paths
   # with actual data.
   
   # Example content for sgRNA_counts.txt (tab-separated):
   # sgRNA_ID\tSample1_Control\tSample2_Control\tSample3_Treatment\tSample4_Treatment
   # sgRNA1\t100\t120\t50\t60
   # sgRNA2\t200\t210\t180\t190
   # ...
   
   # Example content for sgRNA_library.txt (tab-separated):
   # sgRNA_ID\tGene_ID
   # sgRNA1\tGeneA
   # sgRNA2\tGeneB
   # ...
   
   # Example content for design_matrix.txt (tab-separated):
   # Sample_ID\tCondition
   # Sample1_Control\tcontrol
   # Sample2_Control\tcontrol
   # Sample3_Treatment\ttreatment
   # Sample4_Treatment\ttreatment
   
   mageck test \
       -k sgRNA_counts.txt \
       -l sgRNA_library.txt \
       -n mageck_results \
       -d design_matrix.txt \
       --control-id control \
       --treatment-id treatment

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