CDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries.

ABSTRACT:

Background

Exogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. If not properly recognized and managed, this cross-contamination with exogenous signal can lead to incorrect interpretation of research results. Yet, this problem is not routinely addressed in current sequence processing pipelines.

Results

We present cDNA-detector, a computational tool to identify and remove exogenous cDNA contamination in DNA sequencing experiments. We demonstrate that cDNA-detector can identify cDNAs quickly and accurately from alignment files. A source inference step attempts to separate endogenous cDNAs (retrocopied genes) from potential c

SUBMITTER: Qi M 

PROVIDER: S-EPMC8709999 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature