When assembling transcriptomes based on a reference why are the 5' and 3' UTRs commonly lost in the data?
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!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Looking for an old-fashioned alignment editor
written by Suicyte •
-
Conceptual question about open reading frames
written by Daniel •
-
Denovo assembly or Reference based assembly for identifying novel lncRNAs
written by newbie
-
How to select the best isoform for a differential expressed gene in Trinity?
written by upendrakumar.devisetty
-
MUMmer alignments: Trying to understand the average identity result
written by caro-ca •
-
Mapping both PE reads and Single-end reads into transcriptome
written by pbigbig
-
Why we need a distributed assembler based on MPI/Mapreduce when we can store Debruijn graph in a co…
written by saranpons3
-
Possibility of a de-novo assembly but with a gene as starting point/reference?
written by Angelo Victoria •
-
How to annotate coding and long non-coding RNA together using transcriptome data. My idea is to fin…
written by mjoyraj
-
Reassembling Transcriptome Using Recently Published Genome
written by Raghul
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.