cjneely10/EukMetaSanity

How to get nucleotide sequences of predicted genes?

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Hi, I have obtained the protein-coding sequences with respect to the gene numbers. Now I need nucleotide sequences of the adjacent genes. How can I get it? Thank you.

Hi @JSSaini,

EukMetaSanity does not provide this direct feature. For this kind of query, I would consider an outside tool like BEDtools, or using a programming language like Python to develop an in-house tool.

As this is not directly related to EukMetaSanity's features, I will close this issue. Best of luck!

Hi, I have obtained the protein-coding sequences with respect to the gene numbers. Now I need nucleotide sequences of the adjacent genes. How can I get it? Thank you.

Hi, I have obtained the protein-coding sequences with respect to the gene numbers. Now I need nucleotide sequences of the adjacent genes. How can I get it? Thank you.

Hi can use gffread, just input .gff file and genome.fa file. But I found the extracted CDS sequence from Tier.gff or MetaEuk.gff result are longer than the orignal input genome.fa! I was wondering do you have this issue? Many thanks.