[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!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20210627/bbb7450c/attachment-0002.html>