Bioinformatics

Environment setup

• R
  • On MacOS, use brew cask install r-apps rather than brew install r

Reference Genome Build

• Reference genomes and Gene models: Impact on variant interpretation
• Which human reference genome to use?
• hs37d5 information

Misc

• Frequent File Formats
• Installation of samtools
• Human Reference Discrepancies
• BAF
• VCF files: Change Chromosome Notation
• Generate vcf.gz file and its index file vcf.gz.tbi
• Tools for coverage analysis: 1, 2
• WES and RNA-seq difference
• BAM Tricks
• How to check if duplicate reads are marked in bam file?

Manuscript-related

• Which Font Looks Best in a Figure?
• How to write a manuscript by Springer Nature
• Rainbow Color Map (Still) Considered Harmful
  • Related materials:
    • viridis, magma, plasma, and inferno are colormaps recommended to be used in R.
    • for automatic alignment in R:
      • ggplot facet layout: facet_wrap
      • Cowplot::plot_grid
      • gridExtra::arrange.grid