I am yet to try Oases, but curious about what it exactly does. Most importantly, will it join contigs that are output from a velvet assembly(even if they data is single end). Or does it simply cluster sequences with similar regions (e.g. same exons) into clusters, and assigns loci & transcript IDs to these clusters?? Basically, will Oases create longer contigs from my velvet assembly?
It seems like the best technique for transciptome assembly is the multiple k-mer method. But all the papers I read simply use the output of velvet when merging. Would it be smarter to run oases after each velvet run, and then merge the oases output instead??
It seems like the best technique for transciptome assembly is the multiple k-mer method. But all the papers I read simply use the output of velvet when merging. Would it be smarter to run oases after each velvet run, and then merge the oases output instead??
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