STAR.allsteps.multiQC {ORFik} | R Documentation

## Create STAR multiQC plot and table

### Description

Takes a folder with multiple Log.final.out files from STAR, and create a multiQC report. This is automatically run with STAR.align.folder function.

### Usage

    STAR.allsteps.multiQC(folder, steps = "auto", plot.ext = ".pdf")

### Arguments

`folder` | path to main output folder of STAR run. The folder that contains /aligned/, "/trim/, "contaminants_depletion" etc. To find the LOGS folders in, to use for summarized statistics.
`steps` | a character, default "auto". Find which steps you did. If manual, a combination of "tr-co-ge". See STAR alignment functions for description.
`plot.ext` | character, default ".pdf". Which format to save QC plot. Alternative: ".png".

### Value

data.table of main statistics, plots and data saved to disc. Named: "/00_STAR_LOG_plot.pdf" and "/00_STAR_LOG_table.csv"

### See Also

Other STAR: `STAR.align.folder()`, `STAR.align.single()`, `STAR.index()`, `STAR.install()`, `STAR.multiQC()`, `STAR.remove.crashed.genome()`, `getGenomeAndAnnotation()`, `install.fastp()`

[Package ORFik version 1.12.13 Index]