[mira_talk] Re: Mira results much worse than newbler
- From: Robin Kramer <kodream@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 15 Jul 2011 14:05:30 -0600
sff_extract must have been broken when I used it then, because all it did
was mark the first 4 bases as clipped.
Sincerely yours,
Robin
On Fri, Jul 15, 2011 at 1:54 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Jul 15, 2011, at 21:32 , Robin Kramer wrote:
> > Sure, they also say 454 data doesn't have adapters in it.
> >
> > " By default, the trimmed data is output,
> > unless the -notrim output is specified. Only one of -seq, -qual,
> -flow
> > or -mft may be specified (the program uses the last on the
> command-line."
>
> *sigh*
>
> Yes, the above statement - right from the sffinfo documentation if I'm not
> mistaken - is correct.
>
> As well as is what you've been told now a couple of times: sffinfo does not
> do the clipping process! sffinfo converts!
>
> What sffinfo does is to read the SFF file and output the sequence which is
> found in these files. Per default, it outputs the part of the sequence which
> some other Roche processing software defined as good and where the clipping
> point have been stored in the SFF as clipping points. Have a look at the
> public format definition at the NCBI:
>
>
> http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff
>
> and there especially the section on read headers:
>
>
> http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff-2
>
> where you will see that each read has two clipping points defined (quality
> left/right and adaptor left/right). These clipping point are calculated by
> some other software and stored in the SFF.
>
> sffinfo just converts the binary SFF format into something else and it
> applies the clipping points it finds in the SFF ... it does not compute them
> (I have the eery feeling I start to repeat myself here).
>
> And to close the circle: sff_extract does exactly the same as sffinfo ...
> no own clipping, merely reading the data from SFF and convert it to
> something else. And the clipping points are either saved to XML or applied
> by hard-clipping if the user wishes it that way (option -c if I recall
> correctly).
>
> So, the "cleaning" process of sffinfo and sff_extract is 100% identical,
> and where things are identical there can be per definition no difference, no
> inferior- nor superiority.
>
> Have I been able to finally make the process understandable now?
>
> B.
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