Question: Tools for downsampling/resampling/subsampling Oxford Nanopore reads
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gravatar for nkuyfq
5 weeks ago by
nkuyfq60
China
nkuyfq60 wrote:

I have got ~40000 MinION reads derived from a virus, whose read length ranges from ~100 to ~34.9k. I would like to re-sample these reads to evaluate the minimum read number enough to detect this virus. As Oxford nanopore reads have no identical read length, I have to take the varying read length into consideration when re-sampling the reads. Are there open soure tools available for this task?

nanopore • 127 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by nkuyfq60

As Oxford nanopore reads have no identical read length, I have to take the varying read length into consideration when re-sampling the reads.

I'm not sure you have to. Can you elaborate on why you think you have to?

Do you want to evaluate for how long you should have been sequencing?

ADD REPLYlink written 5 weeks ago by WouterDeCoster41k

I want to explore the lower threshold of the read number, like 1000, 1500 or 2000, which is sufficient to identify the target virus. Unlike next-generation sequencing platforms generating reads with uniform read length, MinION-generated reads might own some sort of distribution in read length. In order to aviod the potential bias, I would like to take the varying read length into consideration. Under some extreme conditions, I am afraid I might get reads all longer than 20k or all shorter than 1k after the re-sampling task.

ADD REPLYlink written 5 weeks ago by nkuyfq60

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

If you get a random sample reads from an unequal distribution of reads then you will get the same distribution afterward if you get enough reads.

ADD REPLYlink written 5 weeks ago by WouterDeCoster41k

@WouterDeCoster, due to some currently insoluble issues about the internet services, I am unable to use the ADD COMMENT or ADD REPLY to response to you.

I will try to re-sample the MinION reads as you suggested.

nkuyfq@163.com

From: WouterDeCoster on Biostar Date: 2019-09-11 18:00 To: nkuyfq Subject: [biostar] Tools for downsampling/resampling/subsampling Oxford Nanopore reads Activity on a post you are following on Biostar User WouterDeCoster wrote Comment: Tools for downsampling/resampling/subsampling Oxford Nanopore reads: Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked. If you get a random sample reads from an unequal distribution of reads then you will get the same distribution afterward if you get enough reads.

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ADD REPLYlink written 5 weeks ago by nkuyfq60
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