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Trace Quality Clip

Filename
trace_clip.p4m

Description
This module determines where the sequence quality is too poor to use for reliable assembly. This uses the trace_clip program which reads and writes to Experiment Files. Its quality evaluation is based on analysis of the chromatogram files. Both 5' and 3' ends may be quality clipped. For more details see the trace_clip and scale_trace_clip documentation (see section Trace Clipping). Note that the Phrap assembly algorithm works best without quality clipping and it can make use of the full length of readings (due to the use of the Phred confidence values).

Option: Ends to clip
This controls whether 5', 3' or both ends should be quality clipped.

Option: Maximum right clip
The largest allowable 3' clip point.

Option: Minimum left clip
The lowest allowable 5' clip point.

Option: Start point
The base number from which to search (in both directions) along the good data. If this is set to -1 the program will pick a sensible start point.

Option: Trace_clip arguments
This defines any additional command line arguments to send to the trace_clip program.

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_14.html