Processing
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.
How do I use UMIs for error correction?
Depending on your sample type or experiment goals, you can choose to use UMIs or ignore them altogether.
The xGen™ cfDNA & FFPE Library Prep Kit Analysis Guidelines leads you through the recommended analysis pipeline using open-source tools starting with FASTQ files and resulting in variant calling.
As an overview, fixed UMI sequences, such as those used with the xGen cfDNA & FFPE Library Prep Kit, enable identification and correction of sequencing or PCR errors, even if they appear within the UMI sequence.
- Single-read families analysis: UMIs can also be used to correct errors in sequencing data at the same time as removing duplicate reads. For example, all reads with the same start-stop position and UMI can be grouped as a single-read family then collapsed. Rather than simply choosing the highest quality read, this method uses all reads within the single-read family to choose the most likely base at each position from beginning to end. This process yields a collapsed single-read family that can be used for variant calling. This approach is taken by the tools GroupReadsByUmi plus CallMolecularConsensusReads (fgbio).
Figure 1. Schematic of error correction methods with UMIs.
Categories:
Next generation sequencing*RUO—For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.