[mira_talk] Re: Mira results much worse than newbler
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 15 Jul 2011 21:54:25 +0200
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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