AllClasses: Rolexa Setup Class

In Rolexa: Statistical analysis of Solexa sequencing data

Description

A class holding parameters for subsequent run of Rolexa algorithms

Slots

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.

Author(s)

Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef

References

Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431

See Also

DeCorrelateChannels, DeCorrelateCycles, and TileNormalize

Rolexa documentation built on Oct. 5, 2016, 4:38 a.m.