Rolexa (version 1.28.0)

SaveResults: SaveResults

Description

Read and write data in a convenient form for Rolexa base-calling

Usage

"SaveResults"(run=Rolexa.env,results,outpath,prefix="rs_")
SaveResults(run,...)
"CombineReads"(run=Rolexa.env,path,pattern="s_[1-8]_0[01][0-9]*_seq*")
CombineReads(run,path,...)
"CombineFastQ"(run=Rolexa.env,path,pattern="s_[1-8]_0[01][0-9]*",sext="_seq*",pext="_prb*")
CombineFastQ(run,path,...)

Arguments

run

a RolexaRun object defining the run parameters

results

a results list, as given by FilterResults or SeqScore

outpath

a directory name for the output files

path

a SolexaPath object

prefix

a prefix string for output file names

pattern

a pattern for selecting Solexa output files, see readXStringColumns

sext

file extension tag for sequence files readPrb

pext

file extension tag for prb files, see

...

additional arguments, ignored

Value

CombineReads returns a ShortRead object, CombineFastQ returns a ShortReadQ object,

Details

CombineReads reads "\_seq" files and splits the columns to create a ShortRead object, CombineFastQ reads "\_seq" and "\_prb" files and combines them into a ShortReadQ object, SaveResults creates a ShortReadQ objects from the output of FilterResults and writes it to a file using writeFastq.

References

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

See Also

readFastq to read fastq files, SeqScore and FilterResults to produce results for SaveResults