Comments (3)
The genbank references that I'm looking have a different length segments than the current genbank references: https://www.fludb.org/brc/fluStrainDetails.spg?strainName=A/Perth/16/2009(H3N2)&decorator=influenza
I don't think this should be a problem. In HA, for example, it's just an extra 8 nucleotides prior to the start of the coding region. I think the alignment should eliminate any length differences in our sequences . Does that sound correct to you @trvrb?
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This is fine, you should see that the CDS
annotation shifts appropriately however: https://www.ncbi.nlm.nih.gov/nuccore/GQ293081?%3Fdb=nucleotide
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See note here #13 (comment). This will require modifying a few other config files and can wait a bit.
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Related Issues (11)
- Filter cluster output HOT 5
- Genome reference
- Missing header information in genome reference HOT 1
- Nucleotide length in reference .gb file HOT 3
- Create reproducible coloring for census tracts
- Make filter-to-region optional in extract_cluster_fastas.py HOT 1
- Include script to hide ancestral nodes based on cluster designation HOT 4
- Compare genetic distance to geographic distance
- Calculate genetic distance to closest sample HOT 1
- Clean up incoming ID3C data HOT 11
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