Hi all,
I am trying to get .fasta files for each CDS in a .gtf file and the most obvious way I can find of doing it is to use gffread and the target genome. However, I am wondering if anyone knows how gffread deals with heterozygotes. For SNPs I assume it uses the IUPAC ambiguity codes which is fine by me, but what about heterozygous indels? I don't have many of them in my genome but I like knowing what the tools I'm using actually do rather than just treating them as a magical black box.
Cheers
I am trying to get .fasta files for each CDS in a .gtf file and the most obvious way I can find of doing it is to use gffread and the target genome. However, I am wondering if anyone knows how gffread deals with heterozygotes. For SNPs I assume it uses the IUPAC ambiguity codes which is fine by me, but what about heterozygous indels? I don't have many of them in my genome but I like knowing what the tools I'm using actually do rather than just treating them as a magical black box.
Cheers
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