NYUNY/NYUAD Bioinformatics training resource

This resource has been generated by the Bioinformatics team at NYU Center For Genomics and Systems Biology in New York and Abu Dhabi. The modules included in these resources are designed to provide hands on experience with analyzing next generation sequencing. Standard pipelines are presented that provide the user with a step-by-step guide to using state of the art bioinformatics tools. Each module includes sample datasets and scripts that can be accessed on NYU’s HPC facility.

Contents:

• Intro to Bioinformatics
  • How sequencing works
  • FastA format
  • FastQ format
  • Quality scores
  • SAM, BAM and CRAM formats
  • BED format
  • VCF format
  • GFF3 and GTF formats
• Transcriptomics
  • Bulk RNA-seq
  • Single-cell RNA-seq analysis with Scanpy
  • Multiome
  • Over-representation analysis
  • Gene set enrichment analysis
• Variant Detection & Annotation
  • Whole Genome Sequencing
• Epigenomics
  • ATAC-seq
  • ChIP-Seq Analysis: From Aligned BAM Files to Differential Binding & Enrichment
  • Single-cell ATAC-seq analysis with PEAKVI
• Visualization
  • IGV
• Programming
  • Python
  • R / RShiny
  • Shell
  • SLURM
• De Novo
  • De Novo Genome Assembly & Annotation
  • De Novo Transcriptome Assembly & Annotation
• Metagenomics
  • Series of Metagenomics Workshop
• Primary Analysis
  • Pheniqs