Computational Genomics Series by OARC

Amarel account: You need an Amarel account to participate in the lab section Apply here as soon as possible.

VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.

To connect to the cluster: Please test and be sure it is working for you. Check the user-guide of how to get on to the cluster.

If you have questions or need help, please contact Janet Chang.

• Introduction to RNA-Seq
  • Issues to consider
  • Experimental design
    (read length, depth, replicates..)
  • Statistics for RNASeq – power analysis
• QC and Raw read QC
  • Daily utilities
  • Fastq QC and Interpretation
  • Quality trim-Trimmomatics
• Read mapping and Read counts
  • Aligners—tophat, bowtie, bwa, Star, HISAT2,
    Salmon
  • HtSeq-count/STAR quantMode geneCounts…
  • Post mapping QC

Lab Exercise: FastQC; seqtk; Trimmomatic; HISAT2;