runStarAlign: Submit a list of files associated with a project for bwa...
In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions
Description
Submit a list of files associated with a project for bwa alignment and deduping
Usage
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runStarAlign(projName, sampleID, fileTable, runName,
outRoot = file.path("/scratch/pschofield/Projects", projName),
outName = "Data/alignment/star", noSub = F, scpIt = T,
starMod = "apps/star/2.5.1b/gcc-5.1.0",
samtoolsMod = "apps/samtools/0.1.19/gcc/4.4.7", refSequence = NULL,
refGenome = NULL, ncores = 16, fqExt = ".fq", pe = T, jm = F)
Arguments
projName
project name
outRoot
output root directory
fileList
list of fastq file
PietaSchofield/plibb documentation built on May 6, 2019, 6:45 p.m.
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Description
Submit a list of files associated with a project for bwa alignment and deduping
Usage
1 2 3 4 5 6 | runStarAlign(projName, sampleID, fileTable, runName,
outRoot = file.path("/scratch/pschofield/Projects", projName),
outName = "Data/alignment/star", noSub = F, scpIt = T,
starMod = "apps/star/2.5.1b/gcc-5.1.0",
samtoolsMod = "apps/samtools/0.1.19/gcc/4.4.7", refSequence = NULL,
refGenome = NULL, ncores = 16, fqExt = ".fq", pe = T, jm = F)
|
Arguments
projName |
project name |
outRoot |
output root directory |
fileList |
list of fastq file |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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