Answers.Body: <p>This paper <a href="https://www.biorxiv.org/content/10.1101/728519v1.full" rel="nofollow noreferrer">https://www.biorxiv.org/content/10.1101/728519v1.full</a> 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.</p>
  
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Answers.CreationDate: 2019-10-15T12:39:25.470Z
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Answers.UserDisplayName: Jay Moore
Answers.Body: <p>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 <code>samtools</code> to extract reads that are aligning to a given genomic region:</p>
  
  <pre><code>samtools view input.bam "Chr?:XX-YY" &gt; output.bam
  </code></pre>
  
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Answers.Text: That's not really what I am looking for. I am looking for ways to map reads onto telomeres, and then maybe see peaks from that. Edited my question slightly for clarity.
Answers.UserDisplayName: Whitehot
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Answers.UserDisplayName: haci
Body: <p>I know that telomeres are highly repeated sequences, but is there any way to retain any reads that map to these regions (on HG38)?</p>
  
  <p>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.</p>
  
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-14T18:21:29.267Z
Comments.Text: 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.
Comments.UserDisplayName: Devon Ryan
Tags: <phylogenetics><genome><chip-seq><repeat-elements><telomere>
Title: Is there any way to align ChIP-seq reads to telomeres?
ThreadText: # Is there any way to align ChIP-seq reads to telomeres?
  
  (Asked by: username_0 on 2019-10-14)
  
  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.
  
  **Tags:** phylogenetics, genome, chip-seq, repeat-elements, telomere
  
  > **Comments:**
  > **username_1**: 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.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2019-10-15. Score: 3 | Accepted answer
  
  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.
  
  
  ---
  
  ### Answer by username_3 on 2019-10-14. Score: 0
  
  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
  
  ```
  
  > **Comments:**
  > **username_0**: That's not really what I am looking for. I am looking for ways to map reads onto telomeres, and then maybe see peaks from that. Edited my question slightly for clarity.  
  
  ---
  
  