16S Barcoding long and short sequences return different BLAST results
When performing 16S amplicon sequencing what should one do if the long and short sequences return different BLAST values both with high bit score, low E value, high % pairwise identity and 100% coverage.
My instinct would be to go with the result of the long sequences as they carry more information including the nested information of the short sequences when both have 100% coverage?
Short
Long
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robert.murphy •
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I'd trust the long sequences more. But why do you have short and long sequences anyway ? Full length, or just limited to regions of 16S ? Are the full length from long nanopore or pacbio reads ?
The short sequences are just regions where there is overlap from the forward and reverse read. Long reads are the total combination of both forward and reverse.