Schmutzi damage estimation for NEBNext® Ultra™ II DNA library kit

[freshspaceoctopus]

Hello, I am currently planning estimating contamination for non-UDG NEBNext® Ultra™ II DNA library kits.

As you see, non-UDG NEBNext® Ultra™ II DNA library kits have different damage patterns: They are removed of their 5' C->T deamination, resulting into a different damage plot.

So, there is a problem in estimating contamination priors. The program would fail to find endogenous contamination estimates.

I used a workaround to calculate entire deamination probabilities using your bam2prof without the endo option, then providing this file as a prior.

When we did naive simulation, this approach often underestimated contamination ( if there was 20% contamination, contamination estimates were about 10%)

My understanding was giving the program a sensible prior, the program will work fine, but maybe there needs to be more work done to actually apply schmutzi for non-UDG NEBNext® Ultra™ II DNA data.

Do you have any suggestions for contamination analysis?

Thank you in advance.

[grenaud]

thank you for the question! There is a possibility of bypassing the initial estimate and supply schmutzi with an estimate. However, be careful, then there is no way of teasing apart the contaminant and endogenous.