Truncated chromosomes issue #7
Description
I am running HiScanner on around 30 cells, but it appears to be dropping regions of the genome in the final results. For example, though I am using a bin size of ~500 kb, chromosome 11 only has three bins in it, appearing as a narrow slice in the CNV and BAF plots. Other chromosomes also appear to be truncated. When I ran HiScanner on a single cell as a test, this did not occur.
Is this due to quality issues with the cells? I noticed that during the ADO step, the suggested minimum bin sizes for individual cells varied widely—some were as low as 50 kb, some as high as 2,000 kb, and two cells even had a suggested minimum bin size of "nan". (I chose 500 kb because if I went with the final suggestion of ~2,000 kb, I ran into an error later in the CNV step where it couldn't find segments with more than two bins.)
Also, is there an option to force the CNV plots to include these dropped bins, or at least to insert a visual blank so the chromosomes are all their proper sizes relative to each other?