Q:

Is there any way to align ChIP-seq reads to telomeres?

I know that telomeres are highly repeated sequences, but is there any way to retain any reads that map to these regions (on HG38)?
I recently managed to find some protein binding to centromeres, which are also mainly repeats. Therefore I wondered if there was any way to pick up signal on the telomeres.
My team and I are investigating binding of a protein complex to DNA and the experimental team reported that they saw it a bit on telomeres, so we were wondering if there was any way to measure this through bioinformatics. If not then it's no problem, we would just like to know.

A:

This paper https://www.biorxiv.org/content/10.1101/728519v1.full examines the mapping of some human telomeric sequences, and indicates that there is something like 130kb missing at the telomeres in the HG38 assembly.  One option might be to take the HG38 assembly, and add some missing telomere sequences as an additional pseudochromosome to the FASTA file.  Then if you used this modified reference to align your reads, you should soon get a feel for the level of telomeric reads in your data set.

