REGISTRATION FORM at the bottom of this page.

Linux, Amarel, and Computational Genomics RNA_Seq Analysis (Parts I & II)

The Office of Advanced Research Computing (OARC, has partnered with the NJ Institute for Food, Nutrition, and Health (IFNH, to host this brief workshop series for students, staff, faculty. The goal is to help everyone make those first few steps toward productively using a Linux cluster for research — all members of the Rutgers community have free access to the Amarel Cluster & are welcome to attend any of the following sessions:


Introduction to Linux     [ SESSION CLOSED – FULL ]

(Monday, Dec 17, 1:00-4:00pm, IFNH Board Room 201):

  • Overview of Linux, what is it and why
  • The terminal emulator and the Bash shell
  • Basic commands and syntax
  • Working with files and directories
  • Permissions for files and directories
  • Using a text editor (nano, emacs, vim)
  • Customizing your environment (editing your ~/.bashrc)
  • Moving files to/from a remote system
  • Basics of shell scripting
  • Getting info about your system
  • Basics of compiling code
  • Installing and running software


Introduction to the Amarel Cluster

(Tuesday, Dec 18, 1:00-4:30pm, IFNH room 205):

  • OARC, the Amarel system, our support and outreach resources
  • High-level overview of research computing, computing in parallel, advanced networking, and storage systems
  • Accessing the cluster & basic organization (login node, compute nodes, storage spaces, network connectivity)
  • Remote access (VPN)
  • Transferring files to & from Amarel
  • Using software modules
  • Job scheduling with SLURM
  • Overview of running jobs (serial, parallel, batch, interactive)
  • Writing a job script
  • Submitting jobs
  • Monitoring job status
  • Running some example jobs
  • Capturing and viewing job output/results
  • Configuring environment variables (editing your ~/.bashrc)
  • Basics of compiling and installing your own software
  • Using Singularity for containers
  • Review of best practices
  • Using GUI-based applications with FastX


Introduction to RNA-Seq Analysis, part I       [ SESSION CLOSED – FULL ]

(Wednesday, Dec 19, 10:00 am – 3:00 pm, IFNH Board Room 201. We’ll take a 1-hr lunch break at noon and you may want to visit Harvest just downstairs for lunch)

  • Issues to consider
  • Experimental design (read length, depth, replicates…)
  • Statistics for RNASeq

QC and raw read QC

  • Daily utilities
  • Fastq QC and interpretation
  • Trimomatics

Read mapping and read counts

  • Aligners—tophat, bowtie, bwa, Star, HISAT2.
  • HtSeq-count/STAR quantMode geneCounts
  • Post mapping QC
  • Visualization

Introduction to R and Bioconductor

  • R & Bioconductor
  • Object and function
  • Basic operation


Introduction to RNA-Seq Analysis, part II       [ SESSION CLOSED – FULL ]

(Thursday, Dec 20, 1:00-4:0pm, IFNH Board Room 201)

Data processing and filtering

  • Data processing– filtering
  • Normalization

Quantification and differential expression

  • Expression quantification
  • Statistical models
  • Multiple test correction

Analysis QC (sample QC)

  • Clustering
  • PCA
  • Heatmap
  • Volcano plot

Functional analysis

  • GO Term annotation and enrichment test
  • Gene set analysis and GSEA
  • Pathway analysis
  • Overview of co-expression/network analysis

Feature name, term and Identifier mapping & conversation

  • g:profiler
  • Esembl Biomart
  • Synergizer
  • PIRC


Important Notes:

(1) Just observing is welcome, but to participate in hands-on activities, you must have an Amarel account setup before the workshop. Please complete our web-based form at least 24 hr before the workshop (do this as soon as possible):

(2) A laptop computer running Windows, Mac OS X, or Linux will be required to participate in hands-on activities. Wireless campus network connectivity will also be required. Other mobile computing systems (e.g., tablets) will work if an SSH client is installed. Windows users must install an SSH client like PuTTY ( or MobaXterm ( Alternatively, Windows 10 users can install the complete Windows Subsystem for Linux (

(3) For the Amarel & RNA-Seq sessions, basic Linux command-line skills will be needed. To get to that level, you can attend the “Intro to Linux” session on Monday, work through our Linux tutorial here:, or work through just about any other basic Linux tutorial available via the Internet.


Register to attend ONE or ALL sessions:

** Only the “Intro to Amarel” sesssion (being held in a large classroom, IFNH 205) is still available.

Please register for that session here: