distinguish between alleles and isoforms in a de novo assembly

distinguish between alleles and isoforms in a de novo assembly

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Let’s say I have a de novo assembly of RNA-Seq reads and I know some contigs belong to a locus. is there a method to find out that any two of these contigs are alleles of each other or are isoforms? (I think a global alignment and mismatches and gaps numbers may help, but I am not sure). Any help is really appreciated.


assembly

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