Imports "*SJ.out.tab" from STAR and transforms the raw output into standardized junction output format.

parse_star_sj(path, keep_unstranded = FALSE)

Arguments

path: The path to STAR SJ.out.tab
keep_unstranded: Logical, to keep junctions without strand annotation. If FALSE (default) junctions without strand annotation "*" are filtered out, otherwise they are considered as two separate junctions with "+" and "-" strand.

Value

A tibble in standardized junction format

Examples


path <-  system.file("extdata", "test_star_SJ.out.tab", package = "splice2neo")
parse_star_sj(path)
#> # A tibble: 7 × 9
#>   junction_start junction_end strand chromosome Gene  class junc_id             
#>   <chr>          <chr>        <chr>  <chr>      <lgl> <lgl> <chr>               
#> 1 12227          12613        +      chr1       NA    NA    chr1:12227-12613:+  
#> 2 12697          13221        +      chr1       NA    NA    chr1:12697-13221:+  
#> 3 12721          13221        +      chr1       NA    NA    chr1:12721-13221:+  
#> 4 15038          15796        -      chr1       NA    NA    chr1:15038-15796:-  
#> 5 15947          16607        -      chr1       NA    NA    chr1:15947-16607:-  
#> 6 156021563      156021694    +      chrX       NA    NA    chrX:156021563-1560…
#> 7 156021792      156021999    +      chrX       NA    NA    chrX:156021792-1560…
#> # ℹ 2 more variables: uniquely_mapping_reads <int>, multi_mapping_reads <int>