# 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.

• If it's hard-masked (NNNNN) in the genome, no tool can map against it in the genome. Think about instead mapping to repeat regions or repeat consensus sequences from repeat masker. Oct 14 '19 at 18:21

As far as I understand from this question and a related previous one, you have performed a ChIP-seq analysis and saw peaks at centromere regions. In that case, you can use samtools to extract reads that are aligning to a given genomic region:
samtools view input.bam "Chr?:XX-YY" > output.bam