Hi, I need to generate a custom reference genome (i.e. reference sequence) for a S.cerevisiae strain I use in the lab, which has some polymorphisms. I´ve done the alignments (bowtie, -v 0) using the genome present in SGDatabase as my reference genome and given the polymorphisms, many reads are discarded when they shouldn't.
So far, I have obtained a .bedgraph file that allows me know the coverage in each region. However, I think the value would be higher using a custom reference genome.
Any idea on how to create my custom reference genome? Is it necessary to first call polymorphisms first? If so, how could this be done?