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Bioinformatics Self Learning Resources

Bioinformatics tools and learning resources relevant to sequencing data and other high-throughput genomic data analysis

Partek Flow

Partek Flow USC-logo  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

 

Webinars

 

2019 Partek onsite training

 

Start using Partek Flow

CLC Gx

For reasons of license and computational hardware resource optimization, we have restricted RNA-seq analysis in our CLC Gx USC-logo 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

 

2019 CLC Gx onsite training recording

 

Start using CLC Gx

Galaxy

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