qualityRNASeQC: Run RNASeQC quality control
In RGLab/RNASeqPipelineR: Construct Standardized pipelines for processing RNASeq data
View source: R/RNASeqPipelineR.R
Description
Pre-run Checklist
1. Are the contig names consistent betwen BAM, Refrence and GTF file?
2. Is the BAM indexed? we index the bam files in the prepareBamFiles
3. Is you reference Indexed? We index the refrence genome before runing the tophat
4. Dose the reference genome have a dict file? we generated the dict file in the createGenomeDict
Usage
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qualityRNASeQC(picard.path = "/home/jdeng/bin/picard-tools-1.110/",
ncores = 6, rna_seqc.path = "/home/jdeng/bin/RNA-SeQC_v1.1.7.jar",
paired = FALSE)
Arguments
picard.path
character specifying an absolute path path to the PICARD software directory.
ncores
integer number of cores for running in parallel
rna_seqc.path
character specifying an absolute path path to the RNASeQC directory.
paired
logical specify whether data is paired. Defaults to FALSE.
RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.
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View source: R/RNASeqPipelineR.R
Description
Pre-run Checklist 1. Are the contig names consistent betwen BAM, Refrence and GTF file? 2. Is the BAM indexed? we index the bam files in the prepareBamFiles 3. Is you reference Indexed? We index the refrence genome before runing the tophat 4. Dose the reference genome have a dict file? we generated the dict file in the createGenomeDict
Usage
1 2 3 | qualityRNASeQC(picard.path = "/home/jdeng/bin/picard-tools-1.110/",
ncores = 6, rna_seqc.path = "/home/jdeng/bin/RNA-SeQC_v1.1.7.jar",
paired = FALSE)
|
Arguments
picard.path |
|
ncores |
|
rna_seqc.path |
|
paired |
|
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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