Question: simulate DNA reads with unique molecular identifiers (UMIs)
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gravatar for biobiu
6 months ago by
biobiu100
United States
biobiu100 wrote:

Hi, I'm looking for a DNA reads simulator which has the ability to simulate reads with UMIs. Is anyone familiar with such a tool? thanks in advance

next-gen genome • 274 views
ADD COMMENTlink modified 6 months ago by i.sudbery5.1k • written 6 months ago by biobiu100
1

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.

ADD REPLYlink written 6 months ago by michael.ante3.3k
1
gravatar for i.sudbery
6 months ago by
i.sudbery5.1k
Sheffield, UK
i.sudbery5.1k wrote:

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.

ADD COMMENTlink written 6 months ago by i.sudbery5.1k
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