hg38 Bowtie2 Index with Pseudoautosomal Regions (PARs) Masked

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.