GSE136908 Processing Pipeline

Publication

Circulation (2020) — PMID 32393053

Dataset

RNA Seq of HMVEC under hypoxia

1. 1

   STAR2.6.0a was used to align reads to the genome with default parameters

   STAR v2.6.0a GitHub

   $ Bash example

   # Install STAR (example using conda)
   # conda install -c bioconda star=2.6.0a
   
   # Define variables
   # Placeholder for the pre-built STAR genome index (e.g., for hg38)
   GENOME_DIR="/path/to/STAR_genome_index/hg38"
   # Placeholder for input FASTQ files (assuming paired-end reads)
   READS_R1="sample_R1.fastq.gz"
   READS_R2="sample_R2.fastq.gz"
   # Prefix for output files
   OUTPUT_PREFIX="sample_aligned"
   # Number of threads to use (a common default might be 8 or more)
   NUM_THREADS=8
   
   # Run STAR alignment with default parameters
   # STAR 2.6.0a was used to align reads to the genome.
   STAR \
     --genomeDir "${GENOME_DIR}" \
     --readFilesIn "${READS_R1}" "${READS_R2}" \
     --runThreadN "${NUM_THREADS}" \
     --outFileNamePrefix "${OUTPUT_PREFIX}_" \
     --outSAMtype BAM SortedByCoordinate \
     --outSAMattributes All

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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

   # Assume Kallisto 0.44.0 is installed and in PATH.
   # For installation, you might use:
   # conda create -n kallisto_env kallisto=0.44.0 -c bioconda -c conda-forge
   # conda activate kallisto_env
   
   # Placeholder for reference transcriptome index (e.g., human GRCh38 cDNA)
   # Replace with your actual index file path
   KALLISTO_INDEX="path/to/your/GRCh38_kallisto_index.idx"
   
   # Placeholder for input RNA-seq reads (assuming paired-end)
   # Replace with your actual input FASTQ files
   READS_R1="path/to/your/sample_R1.fastq.gz"
   READS_R2="path/to/your/sample_R2.fastq.gz"
   
   # Output directory for quantification results
   OUTPUT_DIR="kallisto_quant_output"
   
   # Create output directory if it doesn't exist
   mkdir -p "${OUTPUT_DIR}"
   
   # Run Kallisto quantification
   kallisto quant \
     -i "${KALLISTO_INDEX}" \
     -o "${OUTPUT_DIR}" \
     "${READS_R1}" \
     "${READS_R2}"
   

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Tools Used