Hi! I have been reading the BD single-cell multiomics bioinformatics handbook (https://scomix.bd.com/hc/en-us/articles/360019763251-Bioinformatics-Guides).
For its targeted assays (an assay with 399 immune-related genes), there is an option to "map all of the reads only to the forward strand of the provided reference".
I was wondering under which circumstance that I need to do this. To speed up alignment?
But genes are roughly 1:1 on both reverse and forward strands of the reference, wouldn't this let me lose information?