[mira_talk] Re: caf2phdball
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 26 Oct 2009 23:56:15 +0100
Hi Sven,
Sorry for the avalanche of questions. Brace for impact ;)
On 25 Oct 2009, at 18:43 , Sven Klages wrote:
Yes,you do need an actual file, as this should be opened when you
request it in consed.
I'm a bit confused... what kind of file would you create? A zero-size
file? Can you have "chromatograms" for 454 reads as well?
I think I remember there is a option in consed option that allows to
convert sff to phd files, but does it actually create chromatogram
files? And how could we deal with read editing in mira? Use a
converted phd file but the original chromatogram?
You need to have some approximate positions for the chromatogram to
be opened correctly.
If you leave all pos at 0, all "peaks" in the chromat are squashed
together and no (normal) editing is possible.
Makes sense...
We do keep our chromatograms in (indexed) tarballs. No filesystem
problem, very fast :-)
I would be interested to know how you create them. And then, do you
directly link to the tarball in the phd file?
Do the numbers (15, 19) in the calculation of $peakpos come from
empirical data?
Yes, I shamelessly copied it from sff2phdball.c (from consed v17
AFAIR).
Well, I guess it should work with consed then ;)
Hope you survived the avalanche... thanks for your help anyway!
Cheers,
Lionel
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