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isgilman / Portulaca-amilis-genome

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Transcriptome assembly #3

Open caseywdunn opened 5 years ago

caseywdunn commented 5 years ago

What is the motivation for assembling the Transcriptome with trinity and translating that, rather than mapping the Transcriptome data to the assembly and building gene models that way?

isgilman commented 5 years ago

If I understand your question correctly, the answer is I'm doing a bit of both. The guided Trinity approach works by first assigning transcripts to specific regions of the genome using the indices from HISAT2. Then, it runs mini, local, de novo assemblies of transcripts, which helps retain isoforms that would potentially be thrown away if we did not do a de novo assembly and instead made a consensus sequence of the transcripts that pile up at a particular locus. Then, I use Transdecoder to translate those isoforms into predicted protein sequences. This hybrid approach of mapping with local assembly should increase the diversity of mRNA and protein isoforms being fed into MAKER later on.