How to validate?

[BoredMa]

Hello, your cwDTW is very fast and valuable. I want to apply your method, but I need to make sure the accuracy of your tool first. In your paper, you mentioned signal labeling, the labeling difference between cwDTW and Tombo is below 15%. Because I'm not very familiar with this aspect, I want to know how to extract alignment information from Tombo's fast5 file, and how to calculate the 15% value. Do you have the corresponding code for my reference?

[icthrm]

Dear BoredMa,

It is Sheng that run Tombo. However, I have an alternative way to test accuracy. You can use the deepsimulator to generate simulated signals and use cwDTW to align them. The drawing tool can be find in our consequencing paper "novel algorithms for fast accuracy...". Indeed, the accuracy should be around 99% or more if the data is qualified.

Yours,

Renmin Han

BoredMa notifications@github.com 于2020年3月16日周一 下午10:22写道：

Hello, your cwDTW is very fast and valuable. I want to apply your method, but I need to make sure the accuracy of your tool first. In your paper, you mentioned signal labeling, the labeling difference between cwDTW and Tombo is below 15%. Because I'm not very familiar with this aspect, I want to know how to extract alignment information from Tombo's fast5 file, and how to calculate the 15% value. Do you have the corresponding code for my reference?

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[BoredMa]

Thank you for your reply. Have you ever done the comparison experiment between cwDTW and Tombo in running time?

[icthrm]

Dear BoredMa,

Sheng has tried Tombo. If your concern is the alignment between genome sequences and signals, our tool is much fater.

Yours,

Renmin Han

BoredMa notifications@github.com 于2020年3月18日周三 下午9:45写道：

Thank you for your reply. Have you ever done the comparison experiment between cwDTW and Tombo in running time?

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[BoredMa]

Hello, I'm trying to use your tool, but there's a problem. In Tombo, there is a comparison between reference and signal. Does cwDTW need to compare reads to reference, and then intercept the corresponding DNA sequence of reference. Now that I have the SAM file, how can I intercept that DNA sequence?

[icthrm]

Hi,

we do not need the comparison between reads to the reference. We direct compare between signal and read, as our readme in github.

Yours,

Renmin Han

BoredMa notifications@github.com 于2020年4月3日周五 下午10:33写道：

Hello, I'm trying to use your tool, but there's a problem. In Tombo, there is a comparison between reference and signal. Does cwDTW need to compare reads to reference, and then intercept the corresponding DNA sequence of reference. Now that I have the SAM file, how can I intercept that DNA sequence?

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