Bioinformatics Self Learning Resources

Partek Flow   offers a start-to-finish analysis pipeline for bulk RNAseq data analysis. 

• Start with FASTQ files (your own data) or BioProject ID (public data)
• Pre-processing: QA/QC, trimming
• Alignment: STAR, TopHat2, GSNAP
• Quantification: Partek E/M, HTseq-count, Cufflinks
• Differential analysis: Partek GSA, DESeq2, ANOVA

Tutorials

• Partek Flow Quick-start Guide
• RNA-seq workflow tutorial

Webinars

• Introduction RNA-Seq Analysis
• Webinars: Webinar recordings for various NGS data analysis

2019 Partek onsite training

• Training recording - Overview (first half hour offers an overview of Partek Flow)

Start using Partek Flow

For reasons of license and computational hardware resource optimization, we have restricted RNA-seq analysis in our CLC Gx  licenses if the total size of the dataset exceeds 20 GB (.fastq.gz files).  Instead, you are strongly encouraged to take advantage of a powerful and speedy end-to-end solution in Partek Flow.

CLC Gx online tutorials

• New user training:
  • Introduction to CLC Genomics Workbench – part 1
  • Introduction to CLC Genomics Workbench – part 2
• Tutorials
  • Expression analysis using RNA-Seq data
  • All CLC Gx Tutorials

2019 CLC Gx onsite training recording

• Analysis of RNA-seq/microRNAseq data (hands-on)

Start using CLC Gx

The Galaxy project https://usegalaxy.org/ offers a graphic interface to thousands of command-line bioinformatics tools.