Problem creating a reference genome

0

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?

Thanks!!


reference


custom


genome

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