STAR.allsteps.multiQC: Create STAR multiQC plot and table

In ORFik: Open Reading Frames in Genomics

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")

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.

Value

data.table of main statistics, plots and data saved to disc. Named: "/00_STAR_LOG_plot.png" 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()

ORFik documentation built on March 27, 2021, 6 p.m.