Alternate Contigs and Gene expression profiling

[SamCurt]

Currently I do my RNAseq analyses using the primary-assembly-only version of GRCh/GRCm38 from GENCODE, and their annotations thereof.

Upon reading Broad's recent guide on alt-contig-aware variant calling in GATK, I wonder anyone have an idea on whether using the alternate contigs (but staying in the same assembly version) would affect gene expression profiling results?

[dpryan]

There aren't any alt-aware RNAseq aligners (that I know of), so including the alt-contigs will deflate counts of genes on those contigs.