This converts files between the various supported trace formats. At present it
can read ABI, ALF, SCF, CTF and ZTR formats, and can write SCF, CTF and ZTR.
Of these formats, ZTR typically represents the smallest size and is fast due
to its own internal compression routines.
For a table of file sizes coupled
with external compression tools, see
section Compress Trace Files.
The Trace Format Conversion may also be used to apply some simple editing
methods to the traces. These include down-scaling (to reduce file size),
background subtraction, and amplitude normalisation.
- Option: Output format
This selects the format for the output trace files. If the output format is
the same as the input format then the input files will not be
overridden. Instead new files will be produced with names based on the input
names, generated by replacing (for example) ".scf" with "..scf".
The available output format choices are ZTR, CTF and SCF.
- Option: Downscale sample range
- Option: Range
These select whether to reduce the scale used to store the amplitudes, and if
so to what range. ABI files typically range from 0 to 1600 (which is
approximately 11-bit data). Shrinking this down to 0 to 255 (8-bit) will
usually be visually comparable as the trace displays in Gap4 and Trev are
typically smaller than 255 pixels high, although if the Y scale is increased
differences will still be detectable. The purpose of this is to further reduce
- Option: Subtract background
This attempts to eliminate the trace background by a simple technique of
deducting the lowest of the four amplitudes from all of the four
amplitudes. This is an overly crude method which should only be used when the
preprocessing software included on the sequencing manufacturer's instruments
has not been used.
- Option: Normalise amplitudes
This uses a sliding window to compute the average single strengths. From this
it scales the data to try and provide, on average, more uniform peak heights
along the trace. Again this is a very simplistic method and so it is not
advisable unless their is a problem with the sequencing manufacturer's own
- Option: Delete temporary files
When pregap4 can determine that a trace file is neither the original input or
the final output then it is considered to be a temporary file which may be
suitable for deletion. An example would be using Phred with ABI files and then
converting to ZTR. Phred produces SCF files and so we have ABI to SCF to ZTR,
in which the SCF files may be safely deleted.
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Last generated on 22 October 2002.