plasmidspades copy number
hi, is it possible to predict copy number of plasmids using plasmidSpades? have run it on paired end genome seqs, opened the contigs in geneious software and assembled. how can i use the output data best in geneious and how can i annotate? it does only annotate the restriction sites when using plasmapper thanks a lot a total beginner
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greenhorn •
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To my knowledge, not really.
You will see increased coverage if the plasmid is high copy number vs low copy number for instance, but that's about it. In principle I think it's possible to do, but you'd need multiple runs and some quite good standards I think, and you would basically be able to build up a kind of standard curve of coverage vs copy number. The problem here is that no 2 sequencing runs are ever really the same, so you might get more or less coverage each run, without it actually corresponding to a change in plasmid number.
To annotate, run something like
prokkaby Torsten Seeman.