Resources

Tertiary Analysis - Biological Meaning

• Pathway Analysis
  • IPA (Qiagen - CCR License) Future talk

• Functional Analysis

  • Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp
  • DAVID https://david.ncifcrf.gov/
  • Enrichr https://maayanlab.cloud/Enrichr/

• Other Types of Analysis

  • Genomic Location
  • Transcription Factor Enrichment Analysis
  • miRNA Enrichment Analysis

Software Solutions

CCR staff have access to a number of resources

• Biowulf (Helix) - CIT maintained large cluster with a huge software library (Unix command line)
• CCBR Pipeliner (Biowulf)
• Partek Flow (Local Web Service)
• DNAnexus (Cloud Solution)
• CLCBio Genomic Workbench (Small genomes)

Public sources of RNA-Seq data

• Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/)
• Both microarray and sequencing data
• Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra)
• All sequencing data (not necessarily RNA-Seq)
• ArrayExpress (https://www.ebi.ac.uk/arrayexpress/)
• European version of GEO
• Homogenized data: MetaSRA, Toil, recount2, ARCHS4

NGS File Formats

• Sequence
  • FASTA, FastQ
• Alignment
  • SAM, BAM, CRAM
• Annotation
  • GTF, GFF, BED (BIGBED)
• Graphing
  • WIG (BIGWIG), BEDGRAPH

Utility Programs

• SeqKit
• FastQC, RSeQC, MultiQC
• Cutadapt, Fastp, Trimmomatic, TrimGalore STAR,Bowtie, Salmon
• Samtools, Picard, bedrolls, bamtools
• R, Python
• IGV

Web-Based Tools

• BioJupies - Many analysis functions - generates Jupyter Notebook of results
 (https://amp.pharm.mssm.edu/biojupies/)

• IDEP92 - an integrated web application for differential expression and pathway analysis of RNA- Seq data 


  *(http://bioinformatics.sdstate.edu/idep92/) Both allow analysis of many public datasets*

File Transfer Methods

• Globus (https://hpc.nih.gov/storage/globus.html)
• HPCDME
• BOX
• OneDrive
• (s)FTP
• Network Drives
• Flash Drives

Further Reading

• RNA-seqlopedia - https://rnaseq.uoregon.edu/
• RNA-Seq by Example - https://www.biostarhandbook.com/