RNA Seq - Cloud of Contiguous Reads with Identical Barcodes

Question

[stu9175]

Suppose in a 10X genomics experiment, each bubble is equivalent of the human genome in a fixed length fragments. The genomic fragments in a bubble get a unique barcode, so each bubble gets a barcode. The fragments are broken up, ligated with barcode adapters, and sequenced. When read from a fragment are mapped to the reference, they will appear to form a cloud of contiguous reads. Can we assume that a contiguous cloud of mapped res with identical barcodes is sampled from the same chromosome?

Answer 1

[igor]

The 10x platform partitions the material into the barcoded gel beads ("GEMs"). The way the technology is presented is usually simplified to imply that a single GEM is a single fragment, but that is not actually the case. From the 10x website:

Our GemCode Technology creates a unique reagent delivery system that partitions cells or arbitrarily long DNA molecules (including >100 kb) and prepares sequencing libraries in parallel such that all fragments produced within a partition share a common barcode.

The key part is "all fragments produced within a partition share a common barcode". Thus, a single barcode can have multiple fragments that likely would be from multiple chromosomes.