Description Slots Author(s) References See Also
A class holding parameters for subsequent run of Rolexa algorithms
MinimumTagLength
tags shorter than this will not be saved (15)
SequencingLength
number of cycles of sequencing, used to calculate the number of columns in files (36)
Barcode
number of bases used as barcode at the beginning of the tag (0)
HThresholds
entropy thresholds between 1 and 2-base ambiguities, 2 and 3-base ambiguities and 3-base ambiguity or undecided (log2(c(1.5,2.5,3.5)))
IThresholds
total entropy thresholds, as a function of tag length (log2(4+1:36/6))
PET
paired-end sequencing run (FALSE)
fit
use full EM convergence instead of only one-step optimization (FALSE)
normal
use tile-level normalization before base-calling (TRUE)
decorrelate
use 'cycle'-level decorrelation procedure, 'channel'-level, 'both' or 'none' ('both')
idsep
character separating coordinate fields in sequence headers (":")
verbose
print debug information if >0 (0)
colors
list of colors to use in the plots
These values are set using SetModel
and a list of the slot
values can be retrieved with GetModel
.
Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef
Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431
DeCorrelateChannels
, DeCorrelateCycles
, and TileNormalize
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