[mira_talk] Re: 454 trimming, sff_extract and SFF to traceinfo.xml
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 6 Jan 2011 22:27:04 +0000
On Thu, Jan 6, 2011 at 8:46 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> On Mittwoch 05 Januar 2011 Peter wrote:
>> What puzzles me is why using sff_extract on a typical SFF file (with
>> "quality" clipping points but not adapter clipping points) produces a
>> traceinfo.xml file with vector trimming entries and NOT quality
>> clipping. Is this just a practical solution to the fact that SFF files
>> from Roche seem to just have a single value for quality+adapter
>> clipping so this be simply mapped to separate quality+vector clipping
>> values?
>
> It is a practical solution, yes: it prevents accidents happening should people
> ever use -DP:ure=yes on 454 data without having thought things through,
> because MIRA would then try to expand also into adaptor areas (which it then
> does not know of as they are not marked as adaptors).
That makes good sense.
>> If these two types of information were in the traceinfo.xml
>> file given to MIRA would it take advantage of this distinction?
>
> Yes, but then you really need a good adaptor search to add those values to the
> XML file. I have the feeling that this is not trivial. But if done right, you
> would probably be able to just use the vector clippings and drop the quality
> clippings altogether as -CL:pec is pretty good at finding usable base ranges.
I'll keep that in mind. Right now I'm just looking at marking/removing
some PCR primers from my 454 reads (most of my reads are affected,
so sff_extract helpfully warns me about this).
Thanks,
Peter
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