Question: Calculate Short Read Mapping Sensitivity And Ppv
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gravatar for juniper-
6.6 years ago by
juniper-50
Austria
juniper-50 wrote:

Say I use ART to simulate some short reads with the purpose of evaluating the performance of a mapper like bowtie or bwa. There is an option that will allow me to obtain a SAM file with the correct alignments.

Now let's say that I run an mapper and obtain a SAM file with its mappings.

So now I have two SAM files. One with the correct mappings and one with the mappings as determined by the mapper.

My question is, does anybody know of a script or program that will compare the two SAM files and output a report of the sensitivity and PPV?

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ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 6.6 years ago by juniper-50
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