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There are many mapping tools each with its own specifications. When we have two tools for same purpose how can we say which tool is better? if we consider mapping percentage how accurate is it ?
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I suggest having a look at some review papers to get started. There are lots out there. -
Mapping percentage is not a useful statistic, by itself. In my opinion, the only safe way to evaluate mapping tools is to generate synthetic data with random mutations, in which each read is annotated with the genomic origin, so that you can objectively calculate whether the mapping tool produced the correct output. Furthermore, the evaluation should produce ROC curves so that the results are not biased by sensitivity; without considering the curve, sensitivity is punished. Review papers don't typically use this methodology and I have not seen any that I thought were useful.
BBMap comes with a couple tools that are designed for this analysis - RandomReads (which generates synthetic reads from a specific genome using your custom error profile) and SamToRoc (which generates an ROC curve from a sam file, by parsing the headers generated by RandomReads to determine whether the alignments are correct). I encourage you to use them!
P.S. SamToRoc only works on single-ended reads, because the sam spec requires that paired reads have the same name, which mutates their original names.Last edited by Brian Bushnell; 03-01-2016, 08:15 PM.Comment
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