get_star_align_log_summary: Get alignment summary from the output of STAR program.

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Get alignment summary from the output of STAR program.

Description

STAR is widely used alignment software program for RNA-seq and other high throughput genomics data. Once the alignment finishes obvious question is to know what percentage of the reads mapped to the reference. These information is logged in *Log.final.out file which is one of the several files STAR generates at the end of alignment. This function parse *Log.final.out file and extract the mapping statistics in a dataframe format.

Usage

get_star_align_log_summary(log_file)

Arguments

log_file

a string denoting a path to *Log.final.out file generated by STAR aligner.

Value

a dataframe.

Examples

star_align_log_file <- system.file("extdata" , "a_Log.final.out" , package = "parcutils")
x =  get_star_align_log_summary(log_file = star_align_log_file)
print(x)

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.