SCF Import Format

This reads in data from an SCF file, which are fairly common. While the SCF format was originally designed for sequencing, it can also contain data useful to Genographer. The SCF format defines four channels. One of these will need to contain the a sample consisting of known molecular weight and will be used as the size standard.

Since the SCF file contains no peak data, Genographer will attempt to find the peaks in the size standard and label them. These will then be combined with the normal sizing algorithms.

There are sevelar options that will need to be set for the SCF file to be imported:

1. Data channel
2. Standards channel
3. Sizing Function
4. Standards Used
5. Min Peak Height
6. Min Peak Width
7. Remember Settings

Data channel and standards channel tell Genographer which of the channels in the SCF file contain the data and the size standard, respectively,

The sizing function and size standard serve the same purpose as they do in the ABI files. See ABI Trace for more information.

Min peak height and min peak width control the way Genographer tries to detect peaks in the size standard. Note that Genographer will only detect the peaks in the size standard, and not in the data.

If instructed, Genographer will store the options selected in a file called scf.def. The final option is used to control this.

More information on the SCF format can be obtained from the "Staden Package" website: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_toc.html