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Question: Minion reads error rate for indels and snps
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Dear All,

How can I analyze the error rate of my Minion reads? how to calculate the error rate of insertion, deletion and Substitutions? thankT

ADD COMMENTlink 9 months ago tarek.mohamed • 250
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You'll need to align your reads it to a reference genome and then do variant calling. Then check vcf file for insertions, deletions and substitutions. But be careful, the insertions and deletions in nanopore reads for homopolymer sequences are usually wrong.

ADD REPLYlink 9 months ago
BioinformaticsLad
• 120
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Hi, I have the vcf file, but I wonder how can I do the actual error rate analysis?

Thanks

ADD REPLYlink 9 months ago
tarek.mohamed
• 250
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Error rate for the reads? Check out NanoPlot

ADD REPLYlink 9 months ago
BioinformaticsLad
• 120
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If you're talking about the error rate for the SV calls, then you'll need a truth set to compare your calls with known SV calls. This assumes that such a truth set exists.

ADD REPLYlink 9 months ago
BioinformaticsLad
• 120

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