I am planning a whole genome sequencing experiment and will be performing the analyses for the first time. I have studied the analyses of WGS data yet most tutorials or workflows begin with indexing a reference genome from an online database. I am seeking advice on if I should use a experimental control as my de novo genome or to use a reference genome and compare conditions to control after analyses. The sequencing is of a human Podocyte cell line with three experimental conditions. The podocyte cell line was gfp tagged via crispr and sorted which gives two cell lines and/or conditions: GFP+ and GFP-. The third condition is a crispr gene knockout of a close homolog of the gfp tagged gene. The untreated podocyte cell line from which all other cells where generated is what I am considering and using as my experimental control. Should I build a de novo genome with these reads from the control or use a reference genome?
Would greatly appreciate any advice, thanks.