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:
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.
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!
Yi
