Extract CDS from maker gff
I have annotated several genomes using the Maker2 pipeline with the goal of estimating dN/dS ratios for many genes. I have the gff files, and I would like to extract just the coding sequences into a fasta file. Previously I have been using the
fasta_merge script that comes with maker, but I just noticed that the nucleotide sequences that it outputs includes the 5' and 3' UTRs and they are not always in the correct reading frame, which leads to some alignment issues in downstream steps.
Is there a script similar to
fasta_merge but which will output CDS sequences in-frame (cutting off incomplete codons) and without UTRs?
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