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Kathleen Keough edited this page May 21, 2018 · 6 revisions

ExcisionFinder defines a gene as targetable in an individual for allele-specific excision if it has at least two allele-specific sgRNA sites that are predicted to disrupt at least one coding exon. To implement this, we need to have the coding exons annotated for each gene. Here is how you get that gene annotation file. This page is intended to support the code in this Jupyter notebook

Settings for UCSC browser to get NCBI RefSeq annotations for GrCh37:

Settings for UCSC browser to get NCBI RefSeq annotations for GrCh38:

We have tested this with human reference genome GrCh37 and GrCh38.

Other instructions are in the Jupyter notebook. Please don't hesitate to contact us with any issues/questions.

AlleleAnalyzer. Keough et al. 2019, Genome Biology.

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