Why sometimes map all of the reads ONLY to the forward strand of the provided reference?

Why sometimes map all of the reads ONLY to the forward strand of the provided reference?

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Hi! I have been reading the BD single-cell multiomics bioinformatics handbook (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?


Targeted


RNA-seq


Rhapsody


BD

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