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I looked for plasmids in my assemblies by looking for contigs with the same sequence at both ends. I was able to verify that some of the contigs were plasmids by PCR and sequencing but I was not able to get a product for most of them though I was not very exhaustive in the primers that I tried. While this method works, I don't know that I would trust that you found circular DNA without a second verification. -
Finding circular DNAs
I've seen a few older threads on this, but no real consensus yet. Anyone have a script or method for finding circular DNAs (*osmids, minicircles) in an assembly? I suppose it's really just as "simple" as discovering the motif which is repeated and the beginning and end of the contig where it's circularized. Anyone attempted anything like this yet?
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
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