RE: [Staden-package] Use of ABI 3730 KB-basecalled traces in Pregap4?

[Edith S. <ed...@bo...>]

I already tried to use the .scf files produced by the
3730 Sequencing Analysis software, v5.1 - but there appear
to be no quality values output ...
And the phd.1 files output do contain incomplete headers..
Applied Biosystems wants to fix the bugs.

But I am still using Staden 2002.0 version, thus : first
thing to do: update to v. 1.4.0/1 package release ;-)


******************************************
Dr Edith Schlagenhauf
Bioinformatics
Institute of Plant Biology
University of Zurich

e-mail: ediths AT botinst DOT unizh DOT ch
******************************************

On Tue, 11 May 2004, Cook, Malcolm wrote:

> Chiming in!
>
> Trev version 1.8b1 for windows, part of "Version-2003.0-beta" does not
> display them when you turn on "Disply confidence".
>
> Attached is a sample .ab1 file.
>
> I think the 3730 data colleciton software can be configured to
> optionally generate a .scf file in addition to the .ab1 (as well as a
> ".phd.1" file such as is liked by phrap), and the .scf file should open
> in trev and display the confidence scores.  I'm checking on this...
>
> Malcolm Cook - me...@st... - 816-926-4449
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, MO  USA
>
>
>
>
>
>
> >-----Original Message-----
> >From: James Bonfield [mailto:jk...@sa...]
> >Sent: Tuesday, May 11, 2004 11:25 AM
> >To: Edith Schlagenhauf
> >Cc: sta...@li...
> >Subject: Re: [Staden-package] Use of ABI 3730 KB-basecalled
> >traces in Pregap4?
> >
> >
> >On Tue, May 11, 2004 at 05:16:15PM +0200, Edith Schlagenhauf wrote:
> >> I tried to use KB-basecalled traces from an ABI 3730
> >> sequencer directly in Pregap4, but "Trace Format
> >> Conversion" obviously does not know about quality values
> >> present in the AB1 file. How do you proceed to
> >> process such data in Pregap4 ?
> >
> >Pregap4 is simply using convert_trace to create SCF or ZTR files from
> >AB1 files. convert_trace in turn uses io_lib.
> >
> >The latest io_lib code does support the PCON field of AB1 files. Is it
> >this record that KB is using to store confidence values in? PCON was,
> >I think, initially added to store phred confidence values when people
> >started asking for a way to upload phred data into BioLIMS.
> >
> >I think that the PCON support should be in the 1.4.0/1 package
> >release.
> >
> >The easiest way to verify this is simply to use trev to view the AB1
> >file to see if the confidence values are there. If so then pregap4
> >should also be working.
> >
> >Could you please email me an example KB basecalled AB1 file so I can
> >verify the latest code works?
> >
> >James
> >
> >--
> >James Bonfield (jk...@sa...)
> >A Staden Package developer: https://sourceforge.net/projects/staden/
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by Sleepycat Software
> >Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to
> >deliver higher performing products faster, at low TCO.
> >http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3
> >_______________________________________________
> >Staden-package mailing list
> >Sta...@li...
> >https://lists.sourceforge.net/lists/listinfo/staden-package
> >
>