[mira_talk] Re: no 3'end
- From: Martin MOKREJŠ <mmokrejs@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 3 Oct 2015 18:51:31 +0200
Hi Yi,
Huang Yi wrote:
Hello,
Question again. I am working on a small virus genome now. The data are illumina reads.
When I used denovo assembly, mira quickly made a strain, which share over 95% nucleotide
identities with a reference virus genome. But that denovo assembled strain didn't contain
3'UTR. If I used reference assembly, mira gave me a "complete" strain, which is
highly similar to reference (~99%). Many reads can map to reference genome's 3'UTR
region very well, which is around 600nt.
You did not say whether it is a virus with circular or linear genome. Also,
provided Adrian Pelin proposed inspecting SNPs ... well, first of all, is this
an RNA or DNA virus? You speak of 3'-UTR so I guess it is a +RNA virus. What is
the target genome length? What coverage you have in do novo vs. mapping modes?
I prefer to trust the denovo assembled strain because that virus were isolated
from a different host. It may not as same as reference. But I am curious that
why mira didn't assemble the 3'UTR region? Does it mean my studied virus didn't
have that 600nt long 3'UTR or there is any parameter I didn't set correctly?
Thanks!
Could be mira discarded the ends of reads because they were too close to
adapters. Did you use some custom adapters for e.g. reverse-transcription of
viral RNA? Did you remove them from your data?
I could also imagine it was a virus with a circular genome but assembled in a
linear assembly mode - or mira discarded reads which seemed to map to both
linear ends. You should provide more details.
Martin
--
Martin Mokrejs, Ph.D.
Adapter/artefact removal from datasets based on the following technologies:
454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
http://www.bioinformatics.cz/software/supported-protocols/
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