RolexaRun-class: Rolexa Setup Class
Description
A class holding parameters for subsequent run of Rolexa algorithmsSlots
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.References
Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431