Description Usage Arguments Details Author(s) References See Also Examples
Performs multi-threaded base calling on a collection of intensity files generated by the Solexa image analysis software
1 2 3 4 |
run |
a RolexaRun object defining the run parameters |
path |
a SolexaPath object defining providing the input paths |
outpath |
the path to the output directory |
prefix |
output file prefix, see |
nthreads |
number of threads to use |
nfiles |
number of input files to concatenate in one batch |
lane |
the lane number to analyze |
tiles |
a subset of tiles to read |
... |
further arguments passed to the RolexaRun constructor |
The function ForkBatch
runs through the list of input files, concatenates them by
batches of nfiles
, then calls
OneBatch
in each of the
nthreads
threads until all batches have been processed. Each
batch results are passed to FilterResults
and saved in an
output file inside outpath
.
Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef
Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431
CombineFastQ
, CombineReads
and SaveResults
1 2 3 4 5 6 7 8 | path = SolexaPath(system.file("extdata", package="ShortRead"))
rolenv = SetModel(idsep="_")
## Not run:
#This will take some time to complete:
library(fork)
ForkBatch(run=rolenv,path=path,tiles=1)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.