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.