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()

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