Issue with Alignment Results Using Soft-Masked Genome in Bismark

[Chanspace]

I am currently conducting Whole Genome Bisulfite Sequencing (WGBS) data analysis using Bismark and plan to utilize a soft-masked genome, where all repetitive and low-complexity regions are marked with lowercase letters.

During the index generation step, I observed that the index created is consistent with the unmasked genome. However, I noticed a significant difference in the results during the alignment step, specifically in the number of uniquely aligned reads. It appears that tools like Bowtie2 ignore the soft-masking, treating the lowercase letters as uppercase during alignment.

Is there a specific parameter or approach in Bismark that would allow me to achieve alignment results with the soft-masked genome that are comparable to those obtained with the unmasked genome? Any guidance or advice would be greatly appreciated!

Thank you!