GSE104502 Processing Pipeline

Publication

Nature structural & molecular biology (2017) — PMID 29106412

Dataset

Short Poly(A) Tails are a Conserved Feature of Highly Expressed Genes

1. 1

   Read counts were quantified using kallisto.

   kallisto

   $ Bash example

   kallisto -h

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2. 2

   These were then aligned to C. elegans genome WS247.

   STAR (Inferred with models/gemini-2.5-flash) v2.7.10a GitHub

   $ Bash example

   # Install STAR (if not already installed)
   # conda install -c bioconda star
   
   # Define paths and reference genome for C. elegans WS247
   # The C. elegans WS247 genome FASTA and GTF/GFF3 files can be obtained from WormBase (e.g., ftp://ftp.wormbase.org/pub/wormbase/releases/WS247/)
   GENOME_DIR="/path/to/C_elegans_WS247_STAR_index" # Directory containing STAR genome index
   READS_R1="input_reads_R1.fastq.gz" # Placeholder for input forward reads
   READS_R2="input_reads_R2.fastq.gz" # Placeholder for input reverse reads (if paired-end, remove if single-end)
   OUTPUT_PREFIX="aligned_to_WS247"
   
   # --- Genome Index Generation (Run this once if the index does not exist) ---
   # Assuming you have the genome FASTA and GTF files for WS247, e.g.:
   # GENOME_FASTA="/path/to/c_elegans.PRJNA13758.WS247.genomic.fa"
   # GTF_FILE="/path/to/c_elegans.PRJNA13758.WS247.annotations.gtf" # Convert GFF3 to GTF if only GFF3 is available
   # STAR --runMode genomeGenerate \
   #      --genomeDir ${GENOME_DIR} \
   #      --genomeFastaFiles ${GENOME_FASTA} \
   #      --sjdbGTFfile ${GTF_FILE} \
   #      --runThreadN 8 # Adjust number of threads as needed
   # ---------------------------------------------------------------------------
   
   # Align reads to C. elegans genome WS247
   STAR --genomeDir ${GENOME_DIR} \
        --readFilesIn ${READS_R1} ${READS_R2} \
        --readFilesCommand zcat \
        --outFileNamePrefix ${OUTPUT_PREFIX}. \
        --outSAMtype BAM SortedByCoordinate \
        --outSAMunmapped Within \
        --outSAMattributes Standard \
        --runThreadN 8 # Adjust number of threads as needed
   
   # Note: For single-end reads, remove the ${READS_R2} from --readFilesIn.

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