[mira_talk] Re: adaptor trim
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 11 Nov 2015 00:11:53 -0500
On 10 Nov 2015, at 21:35 , Huang Yi <huang.y.hy@xxxxxxxxx> wrote:
[…]
I wonder if you all really didn't do adaptor trim? I had a set of illumina
data from Nextera kit. Is the adaptor from Nextera "standard sequencing
adaptor"?
If I didn't trim the adaptor, only 60% of reads can map to my reference. But
if the adaptors were trimmed, 90% of reads can map.
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 can process
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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