Weird biology
Some organisms practice programmed deletion of DNA in somatic tissues and addition of neo-telomeres at deletion sites. This process is called chromatin diminution and occurs in worms, chordates, insects, and ciliates.
Chromatin diminution can result in truncated chromosome arms, with telomeres attached at a previously internal site OR in a change in chromosome number if a chromosome is split into two by an internal deletion.
In either case we end up with mixed signals from distinct karyotypes when trying to identify correct telomere attachment points.
New Feature Proposal
Detect soft-clipped reads within chromosomes that contain telomeric motifs in the clip. These may be neo-telomeres present in a subset of tissues.
This should work if ref assembly represents the germ-line genome.
However, I would imagine that somatic signal would dominate most assemblies. In this case we would be looking for telomere overhangs where most reads contain telo motif, but with a minority of non-telo reads corresponding to the deleted germ-line DNA.
This will be trickier and could perhaps be included as a report or a tutorial example.
Chromatin diminution refs
https://doi.org/10.1093/g3journal/jkaa020
https://doi.org/10.1101/2025.10.23.681605
Expert contacts
@charlottewright & Blaxter Lab
Weird biology
Some organisms practice programmed deletion of DNA in somatic tissues and addition of neo-telomeres at deletion sites. This process is called chromatin diminution and occurs in worms, chordates, insects, and ciliates.
Chromatin diminution can result in truncated chromosome arms, with telomeres attached at a previously internal site OR in a change in chromosome number if a chromosome is split into two by an internal deletion.
In either case we end up with mixed signals from distinct karyotypes when trying to identify correct telomere attachment points.
New Feature Proposal
Detect soft-clipped reads within chromosomes that contain telomeric motifs in the clip. These may be neo-telomeres present in a subset of tissues.
This should work if ref assembly represents the germ-line genome.
However, I would imagine that somatic signal would dominate most assemblies. In this case we would be looking for telomere overhangs where most reads contain telo motif, but with a minority of non-telo reads corresponding to the deleted germ-line DNA.
This will be trickier and could perhaps be included as a report or a tutorial example.
Chromatin diminution refs
https://doi.org/10.1093/g3journal/jkaa020
https://doi.org/10.1101/2025.10.23.681605
Expert contacts
@charlottewright & Blaxter Lab