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

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3.0 years ago

Analeigh • 0

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?

Targeted RNA-seq Rhapsody BD • 515 views

ADD COMMENT • link updated 3.0 years ago by GenoMax 144k • written 3.0 years ago by Analeigh • 0

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Have you looked at the schematics of the kit? Perhaps they are only capturing one specific strand?

ADD REPLY • link 3.0 years ago by GenoMax 144k

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