I'm mapping bisulfite-treated and untreated (control) of total RNA. I expect multi-mapping to several rRNA loci (in E coli there are 7 rRNA loci, for example). When I map untreated samples to a 'normal' genome/transcriptome I do get multi-mapping, but when I map treated samples to a bisfulfite genome/transcriptome I get mapping to only a single locus.
Is mapping to a bisulfite genome/transcriptome problematic with STAR? Is there some parameter I need to adjust when mapping bisulfite RNAseq? (I write genome/transcriptome because I have tried both ways with the same result).