GSE88633 Processing Pipeline — Yeo Lab Publications

Publication

The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors.

Nature communications (2022) — PMID 35781533

Dataset

GSE88633

shRNA RNA-seq from K562 (ENCSR898OPN)

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook

1

See GSM*_README.txt supplementary file linked below

eclip CWL workflow (Inferred with models/gemini-2.5-flash) vunknown GitHub

$ Bash example

# Installation:
# Ensure cwltool is installed:
# conda install -c bioconda cwltool
# Clone the eCLIP workflow repository:
# git clone https://github.com/yeolab/eclip.git
# cd eclip

# The eCLIP CWL workflow (eclip.cwl) requires an input YAML file specifying
# paths to input FASTQ files (replicates and controls), genome reference files (hg38),
# and other assay-specific parameters. The description implies the use of the human genome (hg38)
# and processing of replicates for reproducible peak identification.
#
# Example input YAML structure (eclip_inputs.yaml):
# fastq_files:
#   - class: File
#     path: /path/to/replicate1.fastq.gz
#   - class: File
#     path: /path/to/replicate2.fastq.gz
# control_fastq_files:
#   - class: File
#     path: /path/to/control1.fastq.gz
#   - class: File
#     path: /path/to/control2.fastq.gz
# genome_fasta:
#   class: File
#   path: /path/to/hg38/hg38.fa
# chrom_sizes:
#   class: File
#   path: /path/to/hg38/hg38.chrom.sizes
# gtf:
#   class: File
#   path: /path/to/hg38/hg38.gtf
# adapter_fasta:
#   class: File
#   path: /path/to/adapters.fa
# output_dir: "eclip_analysis_results"
# num_threads: 16 # Example parameter, adjust as needed

# Execute the eCLIP CWL workflow
# Replace 'eclip_inputs.yaml' with the actual path to your input parameter file.
cwltool --beta-dependency-resolvers-configuration eclip.cwl eclip_inputs.yaml

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