Hi all,
In MIRA4 manual (
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_dataprep),
about data preparation, it said:
"4.4. Illumina
Outside MIRA: for heavens' sake: do NOT try to clip or trim by quality
yourself. Do NOT try to remove standard sequencing adaptors yourself. Just
leave Illumina data alone! (really, I mean it).
MIRA is much, much better at that job than you will probably ever get ...
and I dare to say that MIRA is better at that job than 99% of all
clipping/trimming software existing out there. Just make sure you use the
[-CL:pec] (proposed_end_clip) option of MIRA."
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. Because I do not
know the algorithm of MIRA, may I know if MIRA can process the trim before
assembly?
What do the "standard sequencing adaptors" include?
Thank you for your help.
Yi
