Get alignment summary from the output of STAR program.

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)
#> # A tibble: 13 × 2
#>    type                                    val     
#>    <chr>                                   <chr>   
#>  1 Number of input reads                   41936201
#>  2 Uniquely mapped reads number            40090105
#>  3 Uniquely mapped reads %                 95.60%  
#>  4 Average input read length               300     
#>  5 Average mapped length                   298.24  
#>  6 Number of reads mapped to multiple loci 900879  
#>  7 % of reads mapped to multiple loci      2.15%   
#>  8 Number of reads mapped to too many loci 9335    
#>  9 % of reads mapped to too many loci      0.02%   
#> 10 Number of reads unmapped: too short     921464  
#> 11 % of reads unmapped: too short          2.20%   
#> 12 Number of reads unmapped: other         14418   
#> 13 % of reads unmapped: other              0.03%