CrossFilt: a cross-species filtering tool that eliminates alignment bias in comparative genomics studies of primates
Abstract
Comparative functional genomic studies are often affected by biased read mapping across species due to inter-species differences in genome structure, sequence composition, and annotation quality. We developed CrossFilt, a filtering strategy that retains only sequencing reads that map reciprocally between genomes, ensuring that quantification of read counts is based on directly comparable genomic features. Using both real and simulated RNA-sequencing data from primates, we show that CrossFilt outperforms five alternative approaches that are commonly used, resulting in more accurate inference of gene expression differences. Our results underscore how different preprocessing choices can shape downstream conclusions in cross-species functional genomics analyses.
Fields of Study & Subjects
Genomics and Phylogenetic Studies
Genome Rearrangement Algorithms
Genomic variations and chromosomal abnormalities
Publication details
- Journal / source
- Genome biology
- Publisher
- Springer Science and Business Media LLC
- Volume
- 27
- Issue
- 1
- Publication date
- 23 April 2026
- Language
- EN