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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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Start position for ORF #158

Closed XC-Zhai closed 2 years ago

XC-Zhai commented 3 years ago

Hi, Thanks for this fantastic rgi. I got my result. I have two questions about the results when I look into the matrix: (1) For the "Predicted_DNA", is this from my contigs? because I cannot find them from my contigs. (2)For the "start" and "end" position of ORF in contigs, like this:

Contig: OTU_1003 Start: 26285 Stop: 26842

I am wondering how rgi calculates the start position. Because when I use biopython to extract ORF from OTU_1003, I am not sure if the base at start position (26285) should be included or it should be one base after the start position?

Best, Xichuan

raphenya commented 2 years ago

@XC-Zhai RGI uses prodigal to call genes if you provide the nucleotide sequence and it provides the start and stop including the strand. Maybe check strand?