mskcc
Missing segments
Hi! I've just found that we have no information about some segments of chromosomes in the result data frames. For example one of our samples has a segment of chr6:304637-30185857 and chr6:30186422-33593298, but 565 nucleotides between these segments are missing from the results. They are both 2-1 (no change in copy number), so I can't see the point why they are treated as separate segments, since they have same copy number values. Is this OK?
Thanks, Gergo
The start and end points of a segment are the positions of the first and last loci in a segment. The gap between two segments is the gap between the end point of segment and the start point of the adjacent one. We don't interpolate since for targeted sequencing this gap can be large. I can't venture any guess without data as to how two consecutive segments can have the same copy numbers.
