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Trace Format Conversion

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 file size.

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 software.
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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This page is maintained by staden-package. Last generated on 22 October 2002.