Output summary statistics for telomere repeat motif occurrence

[flokraft85]

Hi @Smeds & @zstephens,
Thanks for providing such a nice tool for telomere analysis!
I was wondering whether it would be possible to include summary statistics on the occurrence of different telomere repeat motifs. Since this information is already used for plotting, the underlying data should presumably be available.
Having such statistics could be helpful for comparing samples, for example to assess whether certain samples show more or less variability in telomere motifs. A more advanced extension could be chromosome-arm–specific statistics, although that might not be strictly necessary.
Alternatively, is there already a feature that provides this functionality and I may have overlooked it?

[zstephens]

Good timing, as I'll be making expanding the metrics in the stats.txt file in the next version release. Could you clarify what statistics related to the different motifs would be most useful to you? Like, raw count of each repeat type, their fraction of their associated TVRs?

[flokraft85]

Hi @zstephens ,
Sorry for the delayed response.

Yes, a raw count of each repeat type as well as the TVRs as part of a bulk analysis across all telomeres would be very useful. As a bonus, having this resolved at the chromosome level would be great, as it would allow us to assess whether certain chromosomes are more prone to motif changes than others.

I work in the field of telomere biology disorders, and such an analysis would be extremely valuable for comparing repeat composition changes between healthy individuals and patients.

Best,
Florian