What I can also suggest, is to map your sequenced reads to the reference.
Inspect the coverage and variation, SNPs, this will tell you whether you
need to denovo assemble your genome or if it's identical to the reference,
and where should you see most variation. It will also tell you if the UTRs
are present or not.
On Sat, Oct 3, 2015 at 11:04 AM, Chris Hoefler <hoeflerb@xxxxxxxxx> wrote:
When you say it didn't assemble, do you mean the reads were discarded
(debrislist), or that they are assembled in a different contig? If your
region is highly repetitive, Mira may not have been able to join the
contigs.
On Oct 3, 2015, at 8:17 AM, Huang Yi <huang.y.hy@xxxxxxxxx> wrote:illumina reads. When I used denovo assembly, mira quickly made a strain,
Hello,
Question again. I am working on a small virus genome now. The data are
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.
isolated from a different host. It may not as same as reference. But I am
I prefer to trust the denovo assembled strain because that virus were
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!
Yi
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