Hello everyone! I want to determine the precise positions of breakpoints in sp1 (assembled species). I have a number of long nanopore
.fastq reads from sp2 (unassembled species). The species sp1 and sp2 are closely related. I am aware of the breakpoints' approximative coordinates (coord2-coord1 ≈ 1Mb, coord4-coord3 ≈ 1Mb). (View the image.)
I adopted the following strategy: I cut left and right regions and aligned to these
.fasta files long nanopore reads separately. I thought that there should only have been a few long reads that both alignments shared. And how I believed that there are breakpoints in these reads. But I discovered that these files have about 40k common reads.
Maybe someone has a better idea (tools) or could improve mine! I appreciate it.