triplet error for spliced proteins #55
Comments
|
To solve this issue, I changed the genomic coordinate of the start positions of the first exon (for forward-stranded genes) or the end positions of the last exon (for reverse-stranded genes) based on the phase (8th column). |
|
Greetings @hrrsjeong! Apologies for the delay, as I have been traveling. The issue here is that, for a given gene_id, the nucleotides must 'add up' to a complete set of codons. Here this is not the case, i.e., the exons are: 8983330..8983493=164nt These sum to 464nt, which is not a complete codon set (multiple of 3), i.e., 464/3=154.67 when the remainder should be 0. Thus, it is important to check the gene annotations to make sure it is correct. Is it possible this gene has a frameshift somewhere? And, if you remove this gene, do you get the same error for other gene(s)? Unfortunately SNPGenie will keep giving this error until all genes are an exact multiple of 3. Let me know if that helps! |
Hello,
Thank you for your great work! When I ran a program (within group analysis) I got an error message regarding the codon multiplet issue as below.
WARNING: The CDS coordinates for gene gene-TTC7A in the gtf file do not yield a set of complete codons,
or are absent from the file. The number of nucleotides must be a multiple of 3.
SNPGenie terminated.
I checked the gene-TTC7A in the gtf file and realized that if the 8th column of the first exon of the gene includes non-zero values the error occurred. I was wondering if you consider this while you concat multiple exons. Thanks!
NW_005081548.1 Gnomon CDS 8983330 8983493 . + 2 transcript_id "rna-XM_014264419.2"; gene_id "gene-TTC7A"; gene_name "TTC7A";
NW_005081548.1 Gnomon CDS 8985037 8985205 . + 0 transcript_id "rna-XM_014264419.2"; gene_id "gene-TTC7A"; gene_name "TTC7A";
NW_005081548.1 Gnomon CDS 9002261 9002391 . + 2 transcript_id "rna-XM_014264419.2"; gene_id "gene-TTC7A"; gene_name "TTC7A";
The text was updated successfully, but these errors were encountered: