[maker-devel] Extract CDS sequences without UTRs

[Sarah Baker]

Hello,

I have annotated several genomes using the Maker2 pipeline with the goal of estimating dN/dS ratios for many genes. 

I have been using the fasta_merge script to extract the coding sequences, but I just noticed that the nucleotide sequences that it outputs (in *.all.maker.transcripts.fasta) sometimes include the 5' and 3' UTRs and they are not always in the correct reading frame. Is there a way to output CDS sequences in-frame and without UTRs (eg. so that the contents of *.all.maker.transcripts.fasta could be directly translated to the *.all.maker.proteins.fasta output by fasta_merge)?

Thank you for this great program!

[Carson Holt]

fasta_tool with the —trim_maker_utr option.

—Carson

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