Short read alignment to the genome

[CodeCheong]

Hi,

Nice work on assembling the T2T-CHM13 genome. I am looking to perform RNA-seq using this as it's reference genome. My question is whether short paired-end reads can be used to align against the T2T genome, and whether these reads will be able to traverse the repetitive regions of the genome but also allowing accurate alignment to the 99 exclusive protein coding genes?Thanks!