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TP, FP, TN and FN in error correction reads

Hello,

I want to know how to calculate the TP, FP, TN and FN in the case of error correction?

Thanks

error-correction assembly reads
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updated by Ram Ram • written by midox midox

1 answer

The same way you would calculate them in any case, with a dataset that has known correct results that's then run through the procedure.

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written by Devon Ryan Devon Ryan

I don't have these results. I have just the Reference genome. Do I use the reference genome?

thanks

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updated by Ram Ram • written by midox midox

Yes, you would have to use a reference genome to generate fake data with known properties what would then be error corrected. Ideally you just sequence the reads, but that assumes that the reference is correct (maybe it's a good assumption, maybe not).

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written by Devon Ryan Devon Ryan

Or the best metric is the mapping of corrected reads to the reference genome. Am I right?

thanks

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updated by Ram Ram • written by midox midox

No, then you're adding another layer of processing and confounding things by how well the aligner is able to deal with the reads and the genome.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

I do not have a choice. Otherwise how I validate my corrected reads??

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updated by Ram Ram • written by midox midox

I have the reference genome. So I can map my corrected reads to the reference genome and I see the results of mapping.

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updated by Ram Ram • written by midox midox

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