Tool to find double strand breaks
Hi everyone
Does anyone know a tool to find double strand breaks from a read mapping? They cannot be simply found by coverage drops, because bases to the left and to the right from the break can be covered by quite a lot of reads. Double strand breaks can be found by the absence of reads that span the points of double strand breaks. The task seems to be obvious but I cannot find a tool which is capable of doing this. The sequencing technology is Oxford Nanopore.
I will be grateful for help
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Jean-Karim Heriche
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shelkmike
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I don't think it's that simple because for one DSBs are very rare events. Current methods I know of (see below) use some form of labeling before sequencing. See:
- Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing and Analyzing and interpreting DNA double-strand break sequencing data with corresponding tools
- qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing and corresponding code
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