hg38 Bowtie2 Index with Pseudoautosomal Regions (PARs) Masked
Abstract
Pre-built Bowtie2 index for human genome assembly GRCh38/hg38 with pseudoautosomal regions (PARs) masked on chromosome Y. The PAR regions on chrY are nearly identical to regions on chrX, causing multi-mapping issues in RNA-seq analysis. This index has the following regions masked with N's: - **PAR1**: chrY:10,001-2,781,479 - **PAR2**: chrY:56,887,903-57,217,415 This index is recommended for use with EASTR and other RNA-seq analysis tools to avoid spurious alignments caused by PAR homology.
Fields of Study & Subjects
Genomics and Phylogenetic Studies
Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
Chromosomal and Genetic Variations
Publication details
- Journal / source
- Zenodo (CERN European Organization for Nuclear Research)
- Publication date
- 3 February 2026
- Document type
- Dataset