Question: simulate DNA reads with unique molecular identifiers (UMIs)
0
gravatar for biobiu
2.1 years ago by
biobiu120
United States
biobiu120 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 • 670 views
ADD COMMENTlink modified 2.1 years ago by i.sudbery11k • written 2.1 years ago by biobiu120
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 2.1 years ago by michael.ante3.6k
1
gravatar for i.sudbery
2.1 years ago by
i.sudbery11k
Sheffield, UK
i.sudbery11k 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 2.1 years ago by i.sudbery11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1135 users visited in the last hour
_