Tool to find double strand breaks

Question

[shelkmike]

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

Answer 1

[Jean-Karim Heriche]

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