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Bioinformatic Workflows

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  • Genomics

  • Genome assembly
  • Variant analysis
  • Metagenomics
  • Genetic analysis

  • Transcriptomics

  • Exploratory gene expression analysis
  • RNA-seq analysis
  • Pathway analysis
  • Transcriptome assembly
  • Single-cell expression analysis
  • MicroRNA data analysis
  • Alternative splicing analysis
  • Fusion gene detection

    • RNAseq STAR (Default settings)

    This pipeline performs the alignment of fastq files, from RNA-seq reads, using the STAR aligner. This software is currently the one with the higher accuracies, even though it requires a large amount of RAM (50Gb for the human genome)

    What you should provide

    1. Reads in fastq format (ideally compressed in .gz format)
    2. The organism from which they come from.

    What you will receive

    1. File with the aligned reads in BAM format.
    2. File with gene quantification for the sample.
    3. File with alignment statistics.
    4. Quality control plots representing the various factors affecting sample overall quality

    WARNING: These files are required for followup analysis, such as Principal component analysis, Heatmap analysis, Differential expression analysis and Pathway analysis Visual exploration of the BAM genomic data can be assessed in IGV.

    Software versions

    • STAR v2.7.10a
    • BioBamBam2 v2.0.180
    • RSeQC v4.0.0
    • dupRadar v1.26.1

    Relevant software values (assume default if unspecified)

    • alignSJoverhangMin set to 8
    • alignSJDBoverhangMin set to 1

    Pipeline 🔗

    Methods (Please adapt)