ezComputeBias: compute and plot the GC content and gene-length associated...
In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

ezComputeBias

R Documentation

compute and plot the GC content and gene-length associated bias in RNA-seq data

Description

compute and plot the GC content and gene-length associated bias in RNA-seq data

Usage

ezComputeBias(
  dsFile,
  dsName = NULL,
  param = NULL,
  qcSummaryDir = "/srv/GT/analysis/p2220/RNA-seq-bias-results",
  refBuildMap = getRefBuildMap(),
  minReadsPerSample = 30000,
  maxReadsPerSample = 5e+06,
  minReadsPerGene = 3,
  minPresentFraction = 0.2
)

Arguments

`dsFile`
`dsName`
`param`
`qcSummaryDir`
`refBuildMap`
`minReadsPerSample`
`maxReadsPerSample`
`minReadsPerGene`
`minPresentFraction`

Examples

## needs the following modules loaded module add Tools/samtools QC/Trimmomatic QC/Flexbar Aligner/kallisto
options(error=recover)
require(ezRun)
dsFile = "/srv/gstore/projects/p3082/ISeq_20190425_iSeq35_o5404_DataDelivery/dataset.tsv"
ezComputeBias(dsFile)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.