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mapping of breakpoint

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  • mapping of breakpoint

    I have run some Illumina paired end and Illumina mate pair experiments, to analyze for chromosomal rearrangements in cancer genomics.

    What is the best procedure to pinpoint the exact sequence just at the break?

    I have mapped using BWA, and analyzed using breakdancer, which is all good and very informative. However, I want to make sure that I squeeze as much information out of my reads as possible, before I set up a number of sanger sequencing reactions. Often there can be a short stretch of random or non-mapable bases in the middle of the break. One approach would be to use a de novo aligner for the regions. Have anyone had luck with that?

    All suggestions are welcome!