Bioinformatics

The bioinformatics team provides analysis support for all biological data. The team has a large pool of experience in analysis support from initial data processing and QC through to publication.

As a team, we have analysed more than 1000 high throughput sequencing datasets (including ATAC-seq, ChIP-seq, ChIP-exo, bulk and single cell RNA-seq, MNase-seq, sgRNA-seq and whole genome resequencing) and have contributed to peer-reviews publications and software from the Rockefeller University.

Examples of analysis projects.

• Single cell RNA-seq analysis of changes in gene expression and identication of cell specific pathways.
• Mapping of transcription factor targets from ChIP-seq and correlation of targets with expression from associated Knock Out experiments.
• Evaluation of genes important to survival after treatment using sgRNA-seq.
• Identification of transcript selection, differential exon usage and splicing motifs in RNA-seq data.
• Analysis and visualisation of evolutionary conserved motifs around functional elements.

If you have a question about present or future analysis or require analysis support please contact Thomas Carroll (brc@rockefeller.edu).

To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
Ronald Fisher

The Bioinformatics team provides advice on experimental design and analysis planning at all stages of an experiment. Working with the experimentalist(s) alongside the Genomics facility at early stages in the design allow for the BRC to assist in the construction of appropriate experimental designs and to ensure the desired power may be achieved.

Examples of typical experimental design tasks:-

• Power calculations for RNA-seq.
• Design for differential occupancy of epigenetic factors by ChIP-seq.
• Choice of sequencing parameters for differential splicing analysis.

If you would like to consult on the design or required power of upcoming or present experiments please contact Thomas Carroll (brc@rockefeller.edu).

• Publications