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Frequently asked questions
Our Scientific Applications Support team has assembled a list of frequently asked questions to help you find answers quickly. Filter using one or more categories to focus on specific topics, or use the search bar to perform a text search.
What is the analysis platform that powers the rhAmpSeq™ CRISPR Analysis Tool?
CRISPRAltRations is the analysis platform behind the rhAmpSeq CRISPR Analysis Tool.
This IDT-developed analysis pipeline is used for CRISPR on- and off-target editing analysis of next generation sequencing (NGS) data generated from amplicon sequencing. The analysis platform available through the rhAmpSeq CRISPR Analysis Tool utilizes cloud-hosted computational resources for data processing.
Briefly, the CRISPR workflow is as follows:
1. Read pairs are identified and merged from paired-end sequencing.
2. Reads are binned to the expected amplicons, resulting from targeted amplification library preparation (e.g., the rhAmpSeq CRISPR Library Kit).
3. A Cas-enzyme specific aligner aligns the read to the expected amplicon.
4. Variants are called and summarized.
Although this workflow is relatively common to most software tools that analyze NGS data derived from CRISPR screens, the rhAmpSeq CRISPR Analysis Tool has key improvements that help to enable more correct variant identification, including: a Cas-specific aligner; an optimized default variant identification window; systematically substantiated program parameters that use open source tools to provide high-quality results.
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