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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?

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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.

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  • $\begingroup$ 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! $\endgroup$
    – OrdiNeu
    Commented Jul 7, 2017 at 13:46

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