Beckman Coulter CEQ 8000, User Manual

Page: 216 / 382

Sequence Analysis Procedures
202 CEQ™ 8000 Genetic Analysis System
FASTA
(.fasta)
The FASTA format only applies to the sequence results portion (e.g., text bases)
of analyzed data, and contains a comment line that is used to identify the data.
Along with the text file, a quality values file is also generated (*.FASTA.QUAL)
which lists the quality value for each base. (Quality values correspond to
-10*log10[error rate]). The range for the quality values is 1 to 99. Edited and
inserted bases will have a value of 99. You would use this format, for instance, to
export data into PHRAP.
If the FASTA format is selected the Result Output (Base Sequence) and the
Quality Parameters will be exported automatically if the sample has been
analyzed with a sequence analysis parameter set. If the sample has been analyzed
with a fragment analysis parameter set, nothing will be exported.
For instance, in PHRED, a quality value of 10
means 1 error in 10. A quality value of 20 means an
error rate of 1 error in 100. A quality value of 30
means an error rate of 1 error in 1,000. A quality
value of 40 means an error rate of 1 error in 10,000,
etc. Normally PHRED would export these quality
values into PHRAP. In the case of exporting from
the CEQ System, we bypass PHRED and export
directly into PHRAP.
PHRED
(.phd.1)
The PHRED format will produce two files; a PHRED file and an SCF file. A
PHRED file is a text file composed of a SEQUENCE section containing a
COMMENT and DNA section. The SEQUENCE section also contains the name
of the Analyzed Result that was stored.
The COMMENT section contains the file name of the associated SCF file
(CHROMAT_FILE) that was produced along with the PHRED file. The values
for ABI_THUMBPRINT and PHRED_VERSION are fixed text "N/A." The
values for CALL_METHOD and QUALITY_LEVELS are fixed as "CEQ and
"99" respectively for CEQ 2000. The TIME stamp is the current time at the time
of export.
The DNA section is composed of the base-call (always lower-case), PHRED
Quality Value, and the Peak Index (data point) of the analyzed data contained
within the associated SCF file. Values are separated by spaces.
If the PHRED format is selected the Result Data, Result Output (Base Sequence),
and Quality Parameters will be exported automatically if the sample has been
analyzed with a sequence analysis parameter set. If the sample has been analyzed
with a fragment analysis parameter set, nothing will be exported.
ESD (.esd)
The ESD, electropherogram sample data, format is used to export raw data from
the CEQ System to a third-party software package for analysis. When you select
this option, on the raw data will be exported, and no other information is
included.
Table 71: Sequence Export Options (Continued)
Format Description