Bioinformatics Core

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The purpose of this Core is to provide bioinformatics analysis of transcriptomic, and DNA-protein interactions. Next-generation sequencers have transformed genomic research, yet the analysis of this data remains a bottleneck. Our Core will provide the essential data analysis service to render this data accessible and interpretable to the members of this CORT. The PI and staff of this Core have extensive experience in the analysis of genomic data, as well as familiarity with the underlying biology of the associated projects. Despite the fact that microarray and sequencing cores exist at UCLA, none of these provide data analysis as a service. Therefore the typical biology group that does not have internal computational expertise is often left with data and no ability to interpret it. The Core we are proposing here will remove this impediment so that all the groups within this Program Project will be able to not only collect sequencing data from their samples, but also obtain processed and analyzed data that can be directly interpreted by researchers without computational expertise. This functionality should render genomics research far more accessible to all members of this Program Project. We will also work with more computationally more experienced researchers in each lab of this Program to refine analysis tools. The Aims of this Core are: 1. Analysis of RNA-seq data: we will provide quantification and variant detection analyses of RNA-seq data. 2. Analysis of ChlP-seq data: we will provide the location of peaks, average peak distributions and motifs. 3. Data display on genome browser: in all cases this core will also load genome-wide data onto our installation of the UCSC genome browser so that users can see at single base resolution the data generated from each sample. We will also upload data and analysis tools to the Wiki site for exchange. 4. Data Quality metrics: we will generate quality metrics for sequence data to provide an estimate of the quality of the sample.