James & Edith,
I checked, and, as far as I can tell, the scf files when displayed in
trev 1.8b1 for windows do NOT show quality scores either.
If it helps your purpose, in the mean time I know of one other viewer
that will open ab1 files and display the quality scores. It is free.
It is Finch TV - http://www.geospiza.com/finchtv/download/index.html
>From: Cook, Malcolm=20
>Sent: Tuesday, May 11, 2004 1:15 PM
>To: James Bonfield; Edith Schlagenhauf
>Subject: RE: [Staden-package] Use of ABI 3730 KB-basecalled=20
>traces in Pregap4?
>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 - mec@... - 816-926-4449
>Database Applications Manager - Bioinformatics
>Stowers Institute for Medical Research - Kansas City, MO USA=20
>>From: James Bonfield [mailto:jkb@...
>>Sent: Tuesday, May 11, 2004 11:25 AM
>>To: Edith Schlagenhauf
>>Subject: Re: [Staden-package] Use of ABI 3730 KB-basecalled=20
>>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
>>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 Bonfield (jkb@...)
>>A Staden Package developer: https://sourceforge.net/projects/staden/
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