When assembling transcriptomes based on a reference why are the 5' and 3' UTRs commonly lost in the data?
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8.5 years ago
cxu325 • 0

Compared to genome assembly, why are the UTRs lost when assembling transcriptomes based off a reference?

Is it because UTRs are not as tightly constrained so that they have less sequence conservation than ORFs. Therefore because they change more they don't align as well to the reference? Thanks!

transcriptome reference-based • 1.2k views
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hi, I dont have much experience in de novo transcriptome assembly but I have noted that many times the coverage of a given transcript is biased towards the 3' end. The reason I read was that because decay starts from 5' end and hence comparatively more reads support towards the 3'. So I guess because of some amount of decay (at 5' end) and highly variable regions (mostly at 3' end), the transcript start-end points will be difficult to assemble for the algorithm, as compared to internal constitutive exons.

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