Hi
I am using bwa on paired end illumina reads for identifying inter chromosomal translocation.
I have used breakdancer on the data but non of the proposed inter chromosomal translocations match what I have on my list of suspects (garnered from FISH)
I am looking at the alignment of the regions now manually and I find that there is low coverage in this region.
I am suspecting that the translocation are taking place in homologous regions within the genome.
Would this cause reads to be 'dropped out' from the final bam file if bwa finds equally plausible regions which the read might map?
How should I hunt for evidence for the translocation?
I am using bwa on paired end illumina reads for identifying inter chromosomal translocation.
I have used breakdancer on the data but non of the proposed inter chromosomal translocations match what I have on my list of suspects (garnered from FISH)
I am looking at the alignment of the regions now manually and I find that there is low coverage in this region.
I am suspecting that the translocation are taking place in homologous regions within the genome.
Would this cause reads to be 'dropped out' from the final bam file if bwa finds equally plausible regions which the read might map?
How should I hunt for evidence for the translocation?
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