GSE136907 Processing Pipeline

Publication

Circulation (2020) — PMID 32393053

Dataset

Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

1. 1

   CLIPSeqTool0.1.8 was used to trim the adapaters, align the reads to the genome and perform deduplications

   CLIPSeqTool v0.1.8

   $ Bash example

   # Installation: CLIPSeqTool is not a standard, publicly available tool with known installation methods.
   # It is likely a custom script or an internal tool. Ensure CLIPSeqTool is available in your PATH or provide its full path.
   # Example: /path/to/CLIPSeqTool/CLIPSeqTool.py
   
   # Define input/output files and reference genome
   # Replace with actual file paths for your specific experiment.
   INPUT_READS_R1="sample_R1.fastq.gz"
   INPUT_READS_R2="sample_R2.fastq.gz" # Remove this line if using single-end reads
   REFERENCE_GENOME_FASTA="path/to/reference/genome.fa" # e.g., /path/to/hg38.fa
   REFERENCE_GENOME_INDEX="path/to/reference/genome_index" # Path to aligner index (e.g., STAR index for hg38)
   
   OUTPUT_PREFIX="sample_output"
   
   # Execute CLIPSeqTool to trim adapters, align reads, and perform deduplication.
   # This command is inferred based on the description and common CLIP-seq processing steps.
   # The exact parameters for CLIPSeqTool are unknown, so these are placeholders.
   CLIPSeqTool \
       --input-r1 "${INPUT_READS_R1}" \
       --input-r2 "${INPUT_READS_R2}" \
       --genome "${REFERENCE_GENOME_FASTA}" \
       --genome-index "${REFERENCE_GENOME_INDEX}" \
       --output "${OUTPUT_PREFIX}" \
       --version "0.1.8" # Assuming the tool supports a version flag
   

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2. 2

   Kallisto0.44.0 was used to quantify transcripts abundance in terms of TPM

   Kallisto v0.44.0 GitHub

   $ Bash example

   # Install Kallisto (if not already installed)
   # conda install -c bioconda kallisto=0.44.0
   
   # Placeholder for reference transcriptome FASTA file (e.g., from Ensembl or GENCODE for GRCh38)
   # Replace 'human_grch38_transcripts.fasta' with your actual transcriptome FASTA file.
   # Replace 'human_grch38_transcriptome.idx' with your desired index name.
   # kallisto index -i human_grch38_transcriptome.idx human_grch38_transcripts.fasta
   
   # Placeholder for input FASTQ files and output directory.
   # Replace 'sample_R1.fastq.gz' and 'sample_R2.fastq.gz' with your actual input read files.
   # Replace 'human_grch38_transcriptome.idx' with the path to your Kallisto index.
   # Replace 'kallisto_quant_output' with your desired output directory name.
   
   # Quantify transcript abundance in terms of TPM (default output of kallisto quant)
   kallisto quant -i human_grch38_transcriptome.idx -o kallisto_quant_output sample_R1.fastq.gz sample_R2.fastq.gz
   
   # For single-end reads, use the --single flag and specify mean fragment length (-l) and standard deviation (-s):
   # kallisto quant -i human_grch38_transcriptome.idx -o kallisto_quant_output --single -l 200 -s 20 sample_single_end.fastq.gz

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