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liampshaw / mobile-gene-regions

Analysing the genomic context of mobile genes
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incorrect annotations overlaid #13

Open liampshaw opened 11 months ago

liampshaw commented 11 months ago

Screenshot 2023-08-04 at 10 44 11

NZ_CP072825.1 has OXA-9 rather than OXA-48 in OXA-48-reduced plot (sixth one down above).

the reason is that it has both OXA-9 and OXA-48 present. to overlay annotations, currently use name matching on "OXA" which picks out the incorrect one because it comes first. so therefore these CDS annotations displayed as overlay are not correct. better would be to use the position information:

gff for OXA-48: NZ_CP072825.1 Protein Homology CDS 5502439 5503236

The pipeline has already stored OXA-48 location in output/OXA-48/gene_diversity/OXA-48_seqs.fa: >NZ_CP072825.1 798bp 5502438-5503236 0 diffs

(off-by-one error in start) but this position information could be used for matching.

liampshaw commented 11 months ago

ditto in first OXA-10 reduced: Screenshot 2023-08-04 at 11 01 32