text: user1076: 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, 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?
  
  user292: 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.
  
original_text: 1076: <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>
   292: <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>
  