How can I analyze the error rate of my Minion reads?
how to calculate the error rate of insertion, deletion and Substitutions?
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.
I have the vcf file, but I wonder how can I do the actual error rate analysis?
Error rate for the reads? Check out NanoPlot
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.
You'll have to align the reads and parse the CIGAR string.
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