I used trim_golary. I agree with you. I redo the assembly using
trimmed reads and with -CL:ckar=no. It gave a better result than raw
reads assembly. That looks normal now. Thanks again!
在 2015年11月13日，00:58，Bastien Chevreux <bach@xxxxxxxxxxxx> 写道：
Because, like the manual states, for Illumnina: "MIRA is much, much better at
that job than you will probably ever be ... and I dare to say that MIRA is
better at that job than 99% of all clipping/trimming software existing out
there."
I suspect the trimming you did (what program , what parameters?) was too
harsh, removing way much more than the adapors. Also, when you trim outside
of MIRA, you need to switch off the trimming done by MIRA (-CL:ckar=no) or
else small sequence parts which look like adapters (but are not) might get
trimmed away and that can slightly worsen an assembly.
B.
On November 12, 2015 at 9:08 AM Huang Yi <huang.y.hy@xxxxxxxxx> wrote:
Thanks! I am using MIRA4.9.5. I expected a better assembly result (less no.
of contigs and longer contigs) when input trimmed reads to MIRA. But it
seems to be opposite. I think MIRA did good on this. I just curious why.
