Compare different gene identifiers
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9 weeks ago
nnl • 0

Hey!

I am trying to compare sets of genes with different identifier types. For example, one set with PROKKA ids and one set with NCBI locus IDs.

Is there any way to compare these two sets to find the common genes? I tried the PATRIC ID Mapper, but it didn't work.

genomes identifiers bacterial genes • 270 views
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Assuming you have the gene coordinates from the same input, you can use intersectBed or coverageBed. I think intersectBed with reporting both hits (-wa -wb) followed by comparing the lines with identical corrdinates of A and B should do it

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Hey, thanks for your reply! Unfortunately, I only have the gene identifiers and no other information. That's why I am trying to map them to a commonly-used database to be able to extract further info from there.