simulate DNA reads with unique molecular identifiers (UMIs)
1 answer
I'm not aware of any tool that simulates reads with UMIs, its definitely a problem for those developing single-cell sequencing tools.
We have some code for simulating a set of UMIs that come from an individual molecules (e.g. have the same start and end co-ordinates). Maybe this would be a helpful starting point.
See upto cell 13 in this notebook.
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Hi, this is more like an idea than a fully thought through recommendation:
The Flux simulator implements a step-wise simulation. Maybe it's possible to pause this tool and modify the intermediate files in such a way, that you include UMIs before the PCR simulation.