Align chimpanzee genome
Hi, sorry for the next question, but I'm just getting started in this bioinformatics universe. I am downloading sra from several species close to sapiens for snp and cnv search. I have aligned and mapped Neanderthal and Denisov sequences using H sapiens chromosome 1 as reference. My question is with other primates, should I use the human genome as a reference to align and observe cnv in chimpanzees, or should I index the chimpanzee genome as a reference and align with h sapiens later? Thank you
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If I understand the question, if you want to identify CNVs in primates compared to the human genome, then you use the Human genome as a reference for all of them.
Ok, perfect, it's just that. Thank you.