TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers.

ABSTRACT: Motivation:Counting molecules using next-generation sequencing (NGS) suffers from PCR amplification bias, which reduces the accuracy of many quantitative NGS-based experimental methods such as RNA-Seq. This is true even if molecules are made distinguishable using unique molecular identifiers (UMIs) before PCR amplification, and distinct UMIs are counted instead of reads: Molecules that are lost entirely during the sequencing process will still cause underestimation of the molecule count, and amplification artifacts like PCR chimeras create phantom UMIs and thus cause over-estimation. Results:We introduce the TRUmiCount algorithm to correct for both types of errors. The TRUmiCount algorithm is based on a mechanistic model of PCR amplification and sequencing, whose two parameters have an imm

SUBMITTER: Pflug FG 

PROVIDER: S-EPMC6157883 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature