Ontology highlight
ABSTRACT:
SUBMITTER: Shinder I
PROVIDER: S-EPMC10632439 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
Shinder Ida I Hu Richard R Ji Hyun Joo HJ Chao Kuan-Hao KH Pertea Mihaela M
Nature communications 20231109 1
Accurate alignment of transcribed RNA to reference genomes is a critical step in the analysis of gene expression, which in turn has broad applications in biomedical research and in the basic sciences. We reveal that widely used splice-aware aligners, such as STAR and HISAT2, can introduce erroneous spliced alignments between repeated sequences, leading to the inclusion of falsely spliced transcripts in RNA-seq experiments. In some cases, the 'phantom' introns resulting from these errors make the ...[more]