[Biojava-l] chromatogram question: get confident value of the called base

Thien Nguyen thien.nguyen at berkeley.edu
Wed Aug 5 19:40:50 UTC 2009


Hello all,
I'm new to BioJava. I start using Chromatogram package to read a number of
.ab1 files and save some statistics. Reading the API, I don't see how to
get some sort of quality/confidence metric for each location, but only the
called base and the raw offset numbers. Here is what I know:
 . ChromatogramFactory to create Chromatogram object from a file
 .ChromatogramTools.getDNASequence to get the called bases, or
TraceOffsetArray to get the raw offset array.

Is there an available method that get the confidence of each called bases?

Thank you

Thien Nguyen




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