Bioinformatics

The Genomics and Sequencing Core currently performs RNA-Seq data processing and analysis and identification of HIV integration sites. Single cell RNA-Seq analysis pipeline is under development. We offer downstream analyses of differentially expressed genes from RNA-Seq data (or any gene lists that may be provided by the customer) to identify gene ontologies (GO) and pathways enriched for the genes of interest. We also provide consultations for planned RNA-Seq experiments, including sample source, power, choice of platform, and selection of RNA-Seq parameters based on scientific question (type of library, sequencing depth, etc.) Training on fully established analytical pipelines is available (please contact the Core for details).

RNA-Seq data processing:  raw .fastq files to .csv matrices suitable for analyses

RNA-Seq data analysis (Bioconductor R): differential expression analysis (e.g. EdgeR); analysis of co-expressed genes (WGCNA)

Downstream gene analyses: analysis of enriched pathways and GO terms for the genes of interest

Analysis of HIV integration sites: analysis pipeline to identify LTR-genomic junctions; uses multiple strategies to count unique integrants in the face of alignment and PCR errors, and cumulative integration site database to  eliminate low level contaminants.

Pricing*

*Pricing quoted for non-profit institutions only. "For-profit" corporations should contact the Core for pricing.