Skip to content

NGS Analysis

learn.gencore.bio.nyu.edu

Topics

  • Next-Generation Sequencing Analysis Resources
  • Pre-Requisites
    • Intro to R
    • Introduction to Linux
      • Linux Exercise
      • Nano Tutorials
  • NGS Sequencing Technology and File Formats
    • How Sequencing Works
    • FastA Format
    • FastQ Format
    • Quality Scores
    • SAM/BAM/CRAM Format
    • BED Format
    • VCF Format
    • GFF3 Format
  • Alignment
    • Trimming with Trimmomatic
  • Visualization
  • Variant Calling
    • Pre-Processing
    • Variant Discovery
  • RNA-seq Analysis
    • Aligning RNA-seq data
    • Introduction to R
    • DESeq
    • DESeq 2
    • Gene Set Enrichment Analysis with ClusterProfiler
    • Over-Representation Analysis with ClusterProfiler
    • Salmon & kallisto: Rapid Transcript Quantification for RNA-Seq Data
    • Instructions to install R Modules on Dalma
  • HPC
    • Resources for editing files on the HPC
      • Atom
      • SSH Mounts
      • Neovim
    • SLURM
    • Modules
    • Gencore Infrastructure
      • Gencore Variant Detection Example
      • Software
        • HPCRunner
        • BioX Workflow
  • ChipSeq analysis
    • CHiP-seq considerations
      • Prerequisites, data summary and availability
    • Deeptools2 bamCoverage
    • Deeptools2 computeMatrix and plotHeatmap using BioSAILs
    • Exercise part4 – Alternative approach in R to plot and visualize the data
  • De novo genome assembly
    • Pre-processing and QC
    • Exercise in de novo assembly
    • Individual Commands
  • Single cell RNA sequencing
    • Prerequisites
    • Seurat part 1 – Loading the data
    • Seurat part 2 – Cell QC
    • Seurat part 3 – Data normalization and PCA
    • Seurat part 4 – Cell clustering
    • Loading your own data in Seurat & Reanalyze a different dataset
  • Metagenomics
    • Quality Control
    • Shotgun Metagenomics
      • Taxonomic Classification
      • Functional Analysis
  • Deep Learning using Keras

BADAS

  • Pheniqs
  • Building R Packages
  • Intro to Nextflow
  • JBrowse: Visualizing Data Quickly & Easily
  • Intro to ggplot
  • Taking it further with ggplot
  • Git and GitHub
  • Seurat: Integration and Label Transfer
  • Nextflow + Containerization
  • Containerization with Docker
  • Jupyter Notebook
  • tidyverse
  • Regular Expressions
  • Customizing Your Unix Environment

HPC

Resources

General

Greene (New York Users)

Dalma (Abu Dhabi Users)

Dalma Tutorials

SLURM

Slurm Best Practices

Transfer Files

File Transfer using Rsync

File Transfer using FileZilla

File Transfer between NYUNY and NYUAD

Linux References

Bash Quick References

Previous
Next
Proudly powered by WordPress