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Uncalled Base Clip

Filename
uncalled_clip.p4m

Description
This module determines where the sequence quality is too poor to use for reliable assembly. This uses the clip program which reads and writes to Experiment Files. Its quality evaluation is based on the number of uncalled bases in a given window length. Both 5' and 3' ends may be quality clipped. The method starts from a point in the middle of the sequence and steps outwards in both directions until the data is considered poor quality. For more details see the clip documentation ( see section `Clip' in clip.1). 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: Start offset
The base number to start the the 5' and 3' good quality searches from.

Option: Minimum extent
The lowest allowable 5' clip position.

Option: Maximum extent
The largest allowable 3' clip position.

Option: 3' window length
The window length in which to count uncalled bases.

Option: 3' number of uncalled bases
The maximum allowed count of uncalled bases in a single window length.

Option: 5' window length
The window length in which to count uncalled bases.

Option: 5' number of uncalled bases
The maximum allowed count of uncalled bases in a single window length.


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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_13.html