alignStar: Simple STAR aligner does everything counts junctions and...
In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions
Description
This is a simpler STAR aligner that runs of single fastq files rather than individual lane fastqs from
the HiSeq. There maybe QC advantages of aligning the individual fastqc but sometimes it is just
simpler to merge before the event.
Usage
1
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alignStar(projName, sampleID, inputPath,
outRoot = file.path("/scratch/pschofield/Projects", projName),
outName = "Data/alignments/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 = ".fastq", pe = T)
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
This is a simpler STAR aligner that runs of single fastq files rather than individual lane fastqs from the HiSeq. There maybe QC advantages of aligning the individual fastqc but sometimes it is just simpler to merge before the event.
Usage
1 2 3 4 5 6 | alignStar(projName, sampleID, inputPath,
outRoot = file.path("/scratch/pschofield/Projects", projName),
outName = "Data/alignments/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 = ".fastq", pe = T)
|
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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