Answers.Body: <p>There are homologous regions between X an Y chromosomes: <a href="https://en.wikipedia.org/wiki/Pseudoautosomal_region" rel="noreferrer">https://en.wikipedia.org/wiki/Pseudoautosomal_region</a></p>
  
  <p>It is therefore normal to have some female-derived reads mapping in Y chromosome.</p>
  
  <p>You should probably check what proportion of such reads fall in other parts of the Y chromosome than pseudoautosomal regions.</p>
  
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Answers.Text: This is it -- I just noticed that most prominent peak corresponds to PRKY, a peudogene in the pseudoautosomal region that's similar to PRKX. Not all of my reads in chrY were pseudoautosomal, but all of my MACS2-called peaks were. Thanks!
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Body: <p>I'm working with scATAC-Seq data on the K562 cell line, which is supposed to be derived from a female patient. <a href="https://www.nature.com/article-assets/npg/nature/journal/v523/n7561/extref/nature14590-s1.pdf" rel="noreferrer">While following the scATAC-seq data analysis pipeline</a>, after performing bowtie alignment they recommend filtering out all reads aligned to mitochondrial DNA and on the Y chromosome.</p>
  
  <p>Out of curiosity, I decided to count how many reads aligned to chrY and found that it can be quite high - chrY has approximately 10% as many reads as a similarly-sized chromosome (chr19 in hg19).</p>
  
  <p>Is it normal to find reads mapping to chrY when the cell line is female-derived, or did I mess up somehow?</p>
  
Tags: <phylogenetics>
Title: Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line?
ThreadText: # Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line?
  
  (Asked by: username_0 on 2017-07-07)
  
  I'm working with scATAC-Seq data on the K562 cell line, which is supposed to be derived from a female patient. [While following the scATAC-seq data analysis pipeline](https://www.nature.com/article-assets/npg/nature/journal/v523/n7561/extref/nature14590-s1.pdf), after performing bowtie alignment they recommend filtering out all reads aligned to mitochondrial DNA and on the Y chromosome.
  
  Out of curiosity, I decided to count how many reads aligned to chrY and found that it can be quite high - chrY has approximately 10% as many reads as a similarly-sized chromosome (chr19 in hg19).
  
  Is it normal to find reads mapping to chrY when the cell line is female-derived, or did I mess up somehow?
  
  **Tags:** phylogenetics
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2017-07-07. Score: 7 | Accepted answer
  
  There are homologous regions between X an Y chromosomes: <https://en.wikipedia.org/wiki/Pseudoautosomal_region>
  
  It is therefore normal to have some female-derived reads mapping in Y chromosome.
  
  You should probably check what proportion of such reads fall in other parts of the Y chromosome than pseudoautosomal regions.
  
  > **Comments:**
  > **username_0**: This is it -- I just noticed that most prominent peak corresponds to PRKY, a peudogene in the pseudoautosomal region that's similar to PRKX. Not all of my reads in chrY were pseudoautosomal, but all of my MACS2-called peaks were. Thanks!  
  
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