STAR.allsteps.multiQC | R Documentation |
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.
STAR.allsteps.multiQC(folder, steps = "auto", plot.ext = ".pdf")
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". |
data.table of main statistics, plots and data saved to disc. Named: "/00_STAR_LOG_plot.pdf" and "/00_STAR_LOG_table.csv"
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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