From this link remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline, I have learned that depending on context, it is perfectly valid to remove X and Y chromosomal genes in an RNA-seq dataset before doing differential expression analysis. However I only have access to the count matrix and not the bam files of the RNA seq data I am analysing. Is it advisable to do the X and Y chromosome gene removal at the level of the count matrix? I am talking about removing all rows that contain X and Y chromosomal genes from the .csv count matrix file read in to RStudio before proceeding to create the DESeq2 object.

Thank you in advance for your kind response.

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    $\begingroup$ First off, it can be valid, but why do you want to do so? In my lab we use them as a validation (does sample X that is a male, has gene expression of Y?). I think that removing them leads to more work with unclear benefit: what if there is a relevant gene in the X chromosome? $\endgroup$ – llrs Apr 9 '19 at 13:09
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    $\begingroup$ Why do you want to do this? It is almost never a good idea and will most likely not have the effect that you think it will (e.g., it won't remove gender differences). $\endgroup$ – Devon Ryan Apr 10 '19 at 11:59
  • $\begingroup$ @Devon Ryan : Thank you very much for your response. Do you please have a supporting publication? $\endgroup$ – Charles Apr 11 '19 at 12:04
  • $\begingroup$ No one would ever bother writing a paper about something that is (A) almost never done and (B) rarely useful. $\endgroup$ – Devon Ryan Apr 11 '19 at 12:08

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