GSE276985 Processing Pipeline

Publication

Nature neuroscience (2025) — PMID 40456907

Dataset

Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]

1. 1

   eCLIP data was analyzed using Skipper with default settings.

   Skipper vv0.1.0 GitHub

   $ Bash example

   # Install Skipper (if not already installed)
   # conda install -c bioconda skipper
   
   # Skipper requires a configuration file (config.yaml) to specify input files, genome references, and other parameters.
   # For "default settings", ensure your config.yaml is set up with standard paths and parameters.
   # Example minimal config.yaml content (adjust paths and parameters as needed):
   # wildcards:
   #   rbp: ["RBP_NAME"]
   #   replicate: ["rep1"]
   # # Placeholder for human GRCh38 genome fasta and GTF annotation
   # genome_fasta: "/path/to/human/GRCh38/genome.fa"
   # gtf: "/path/to/human/GRCh38/annotation.gtf"
   # # ... other default Skipper parameters ...
   
   # Run Skipper using the specified configuration file.
   # The --cores parameter can be adjusted based on available computational resources.
   skipper run --configfile config.yaml --cores 8

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2. 2

   The kDa of each ORF was matched to the closest input sample beginning at that range; for example, a 78 kDa ORF would be paired with the input sample covering the range of 75 to 150 kDa.

   Custom script (Inferred with models/gemini-2.5-flash) vN/A

   $ Bash example

   # Create dummy input files for demonstration
   echo -e "ORF1\t78.0\nORF2\t120.5\nORF3\t60.0\nORF4\t160.0" > orf_data.tsv
   echo -e "SampleA\t75.0\t150.0\nSampleB\t50.0\t74.9\nSampleC\t150.1\t200.0" > sample_ranges.tsv
   
   # Python script to perform the matching logic
   python3 -c '
   import sys
   
   def match_orf_to_sample_range(orf_data_file, sample_ranges_file, output_file):
       """
       Matches ORFs by kDa to the closest input sample range.
       Input files are assumed to be tab-separated:
       - orf_data_file: ORF_ID\tkDa
       - sample_ranges_file: Sample_ID\tMin_kDa\tMax_kDa
       Output file: ORF_ID\tkDa\tMatched_Sample_ID
       """
       sample_ranges = [] # List of (min_kDa, max_kDa, sample_id)
       try:
           with open(sample_ranges_file, "r") as f:
               for line in f:
                   parts = line.strip().split("\t")
                   if len(parts) == 3:
                       sample_id, min_str, max_str = parts
                       min_kDa = float(min_str)
                       max_kDa = float(max_str)
                       sample_ranges.append((min_kDa, max_kDa, sample_id))
                   else:
                       sys.stderr.write(f"Warning: Skipping malformed line in {sample_ranges_file}: {line.strip()}\n")
       except FileNotFoundError:
           sys.stderr.write(f"Error: Sample ranges file not found: {sample_ranges_file}\n")
           sys.exit(1)
       except ValueError:
           sys.stderr.write(f"Error: Invalid number format in {sample_ranges_file}\n")
           sys.exit(1)
   
       try:
           with open(orf_data_file, "r") as orf_f, open(output_file, "w") as out_f:
               out_f.write("ORF_ID\tkDa\tMatched_Sample_ID\n")
               for line in orf_f:
                   parts = line.strip().split("\t")
                   if len(parts) == 2:
                       orf_id, kDa_str = parts
                       orf_kDa = float(kDa_str)
                       
                       matched_sample_id = "N/A"
                       # Find the range where orf_kDa falls (inclusive range based on example)
                       for min_r, max_r, sample_id_r in sample_ranges:
                           if min_r <= orf_kDa <= max_r:
                               matched_sample_id = sample_id_r
                               break # Assuming each ORF matches only one range
                       
                       out_f.write(f"{orf_id}\t{orf_kDa}\t{matched_sample_id}\n")
                   else:
                       sys.stderr.write(f"Warning: Skipping malformed line in {orf_data_file}: {line.strip()}\n")
       except FileNotFoundError:
           sys.stderr.write(f"Error: ORF data file not found: {orf_data_file}\n")
           sys.exit(1)
       except ValueError:
           sys.stderr.write(f"Error: Invalid number format in {orf_data_file}\n")
           sys.exit(1)
   
   if __name__ == "__main__":
       # Define input and output filenames
       ORF_DATA_FILE = "orf_data.tsv"
       SAMPLE_RANGES_FILE = "sample_ranges.tsv"
       OUTPUT_FILE = "matched_orfs.tsv"
       
       match_orf_to_sample_range(ORF_DATA_FILE, SAMPLE_RANGES_FILE, OUTPUT_FILE)
   '
   
   # Display the output
   cat matched_orfs.tsv

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Tools Used