Nelakuditi, V. | bioRxiv Science

bioRxiv2020

FORCAST: a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments

Cas-mediated genome editing has enabled researchers to perform mutagenesis experiments with relative ease. Effective genome editing requires tools for guide RNA selection, off-target prediction, and genotyping assay design. While independent tools exist for these functions, there is still a need for a comprehensive platform to design, view, evaluate, store, and catalogue guides and their associated primers. The Finding Optimizing and Reporting Cas Targets (FORCAST) application integrates existing open source tools such as JBrowse, Primer3, BLAST, bwa, and Silica to create a complete allele design and quality assurance pipeline. FORCAST is a fully integrated software that allows researchers performing Cas-mediated genome editing to generate, visualize, store, and share information related to guides and their associated experimental parameters. It is available from a public GitHub repository and as a Docker image, for ease of installation and portability.

bioinformatics↗

bioRxiv2018

OCHROdb: a comprehensive, quality checked database of open chromatin regions from sequencing data

International consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.

genomics↗