Thank you very much for the reply.
Sorry, I may not describe clearly. MIRA didn't miss anything. I was
questioned why didn't trim adaptors before using MIRA. I think MIRA can do
this like what it said in the manual. But the question made me doubt the
assembly because I had never compared the assembly results between using
raw reads and adaptor free reads. So I want to ask to confirm it. I am
happy when you said Nextera adaptors could be trimmed by MIRA. Now, I am
setting up two assemblies and waiting for the results. When it is done, I
will let you know.
My other question is: there is "Num. reads assembled" in file
"info_assembly.txt", which I think shows how many reads were used for MIRA
assembly. This number is less than what I feed to MIRA. Is it possible to
pull those reads out?
Thanks!
2015-11-11 13:11 GMT+08:00 Bastien Chevreux <bach@xxxxxxxxxxxx>:
On 10 Nov 2015, at 21:35 , Huang Yi <huang.y.hy@xxxxxxxxx> wrote:
[…]illumina data from Nextera kit. Is the adaptor from Nextera "standard
I wonder if you all really didn't do adaptor trim? I had a set of
sequencing adaptor"?
But if the adaptors were trimmed, 90% of reads can map.
If I didn't trim the adaptor, only 60% of reads can map to my reference.
Nextera adaptors are part of trimming pipeline and should be removed by
MIRA. If not, I would consider this to be an error. Your 60% vs 90% numbers
seem to clear enough that MIRA misses your adaptors.
I’m in the middle of a move atm and cannot promise you to work on it
immediately, but would it be possible for you to provide a subset of your
data? And also tell me what you used for trimming outside MIRA?
Because I do not know the algorithm of MIRA, may I know if MIRA canprocess the trim before assembly?
Default is to always trim before mapping or assembly.
What do the "standard sequencing adaptors" include?
The sequences are listed in src/mira/adaptorsforclip.solexa.xxd of the
MIRA source.
B.
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