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Old 01-13-2014, 02:52 AM   #1
Location: UK

Join Date: Jun 2012
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Default de novo transcriptome Trinity Assembly concatenamers

Hi all,

I got a de novo transcriptome Trinity assembly of a drosophila species which is evolutionary far from other sequenced species (closest one is pseudoobscura, but 10% divergency at least).
In my assembly I find many big contigs which consist of concatenamers of genomically close genes (see attached fig, my contig is the red stripe aligned to pseusdoobscura genome).
I suppose this is not due to genome contamination since I always find intact, full spliced ORFs inside these contigs.
I also suppose that this is generated by the fact that some genes have overlapping UTRs.
Does someone has already faced this situation and has an idea how to overcome this assembly problem?
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Old 01-13-2014, 04:25 AM   #2
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Yes, we have similar errors. We used genome guided Trinity to minimize this problem. Pasa also can help. You can read this
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Old 01-14-2014, 02:34 AM   #3
Location: UK

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Hi TiborNagy, thanks for your reply...
Can you please tell me how efficient is this method?
What the percentage-ish of resolution of the "multigene" contigs?
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