soft masked decoy

[gjones3339]

Thank you for this wonderful pipeline. I have some human bulk RNAseq samples that were aligned in STAR against the genome with the soft-masked primary assembly (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa).

I want to run Salmon with the full genome decoy to compare, and would like to use the same reference files for consistency. Does Salmon (like STAR) ignore the lower case for these sequences? Or since its the decoy, does it make a big difference?

Thanks.