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More Info
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SCF (.scf)
The
SCF (Standard Chromatogram Format) format is used to store analyzed DNA
sequence or fragment data for a single sample. The format describes
both "public" and "private" data sections. The well-defined public data
section contains trace data points, the called sequence or identified
fragments and the positions of each called base or fragment within the
trace data. A public comment section is also defined. The "private"
section can be used to store other information that will generally be
ignored by most software packages.
The CEQ 8000 uses the
private data section to store sample data (including raw data along
with current and voltage data). Sample data from either sequencing or
fragment analysis samples can be stored. The notes and property sets
are stored in the comment section. The CEQ 8000 software supports SCF
versions 2.1 and 3.0. (You would use this format, for instance, to
export analyzed sequence data into Lasergene's SeqMan from DNASTAR
Inc.).
Use the SCF format to import data from third-party software into the CEQ
system.
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Tab-Delimited Text (.txt)
The
Tab-delimited format is valid for sample data, sequence results,
fragment lists, sample plates, analysis parameters, methods, optical
scan data, and sample plate results.
The data points will be expressed as text values and can be viewed in any text editor or in Excel.
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ESD (.esd)
The
ESD, electropherogram sample data, format is used to export raw data
from the CEQ 8000 to a third-party software package for analysis. When
you select this option, only the raw data will be exported, and no
other information is included.
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DMPopulation (Discovery Manager) *.txt
This
is an export of the Study's pedigrees and genotypes. The DMPopulation
file is designed to be imported into Genomica’s Discovery Manager
application. The DMPopulation file can also be imported into Discovery
Manager as a DMFastPopulation file. The pedigree and genotype
information from each result in the study is included in the
DMPopulation file.
This export produces two files:
• *.txt = the DMPopulation file
• *.log = a list of processing steps and errors encountered during the export.
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CEQ (.cq*)
The
CEQ* format is the CEQ 8000 software format that is valid for sample
data, sequence and fragment results, sample plate results, sequence and
fragment analysis parameters, sample plates, methods, locus tags,
standards, and optical scan data. The header and the run and analysis
logs are exported automatically.
Use this format to
transfer data to and from CEQ 8000 databases to maintain exact copies
of data, including header information.
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FASTA (.fasta)
The
FASTA format only applies to the sequence results portion (e.g., text
bases) of analyzed data, and contains a comment line, which 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.
Note
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 CEQ 8000, we bypass
PHRED and export directly into PHRAP.
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CSV (comma) *.csv
The
data in this export are comma delimited, suitable for viewing in most
3rd party spreadsheet applications. The export format has the *.csv
extension.
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SEQ (.seq)
The
SEQ format only applies to the sequence results portion (e.g., text
bases) of analyzed data. You would use this format, for instance, to
export data into Lasergene's SeqMan from DNASTAR Inc.
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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 SEQUENCING" and "99" respectively for
CEQ 8000. 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.
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Pedin (Linkage) *.pre
This
is an export of the Study’s pedigrees and genotypes. The Pedin file is
designated to be imported into a Linkage application’s MakePed utility
program. The pedigree and genotype information from each result in the
Study is included in the Pedin file. Up to two alleles per locus is
supported. The export produces three files:
• *.pre = the Pedin file
• *.log = the list of processing steps and errors encountered during the export.
• *.debug = the text file with column headings and comma separated data to aid in the correction of errors in the *.pre file.
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