Frequently asked questions

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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 resequencing. The analysis platform¾available through the rhAmpSeq CRISPR Analysis Tool¾utilizes cloud-hosted computational resources for data processing. Briefly, this is the workflow:

  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 enable higher accuracy of variant detection, including:

  • a Cas-specific aligner
  • an optimized default variant detection window
  • systematically-validated program parameters that use open source tools to provide high-quality results


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