[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!


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