Let me try it. Thank you very much.
2015-11-18 12:42 GMT+08:00 Bastien Chevreux <bach@xxxxxxxxxxxx>:
On 17 Nov 2015, at 23:34 , Huang Yi <huang.y.hy@xxxxxxxxx> wrote:
Thanks very much. I do think current contig number is too high. That iswhy I cleaned the data and tried to get some improvements. Is there any
space to improve? The reads are in 30bp-151bp length.
MIRA4.9.5
parameters = -DI:trt=/tmp -NW:cmrnl=no SOLEXA_SETTINGS -CL:pec=no
readgroup = Data
autopairing
data = ./45x_1.fastq ./45x_2.fastq
technology = solexa
template_size = 300 700 autorefine
Not really much space to improve with the data you have I think. Leave out
the “template_size” line, autopairing normally is pretty good at finding
out what the real size distribution is. If you absolutely want that line,
be a bit more forgiving. E.g.:
template_size = 50 1000 autorefine
Reason is: MIRA will never lower the left boundary and it will never
increase the right boundary. So if you get these estimates wrong, things
cannot be corrected anymore by autorefine.
B.
PS: if you need a “good” assembly, use PacBio and polish with Illumina.
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