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Read base-calling error ("bcerror") TSV files.

Source: R/read-bcerror.R
read_bcerror.Rd

bcerror files are generated by the tRNA sequencing pipeline. Each file contains per-position error rate statistics for a single sample.

Usage

read_bcerror(bcerr_path)

Arguments

bcerr_path

Path to bcerror file.

Value

A tibble

Details

Columns returned:

  • ref: reference tRNA name

  • pos: position in reference (1-based)

  • cov: coverage (spanning reads)

  • a_freq, t_freq, g_freq, c_freq: nucleotide frequencies

  • mis: mismatch frequency

  • ins: insertion frequency

  • del: deletion frequency

  • error_rate: total base-calling error (mis + ins + del)

  • mean_qual: mean base quality at position

Examples

bcerr_path <- clover_example(
  "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.bcerror.tsv.gz"
)
read_bcerror(bcerr_path)
#> # A tibble: 1,404 × 12
#>    ref        pos   cov a_freq t_freq g_freq c_freq   mis   ins   del error_rate
#>    <chr>    <int> <dbl>  <dbl>  <dbl>  <dbl>  <dbl> <dbl> <dbl> <dbl>      <dbl>
#>  1 host-tR…     1     0    0        0   0      0     0        0     0       0   
#>  2 host-tR…     2     0    0        0   0      0     0        0     0       0   
#>  3 host-tR…     3     0    0        0   0      0     0        0     0       0   
#>  4 host-tR…     4     1    1        0   0      0     0        0     0       0   
#>  5 host-tR…     5     1    1        0   0      0     0        0     0       0   
#>  6 host-tR…     6     1    0        0   1      0     0        0     0       0   
#>  7 host-tR…     7     1    1        0   0      0     0        0     0       0   
#>  8 host-tR…     8     2    0.5      0   0.5    0     0.5      0     0       0.5 
#>  9 host-tR…     9     4    0        0   0.25   0.75  0.25     0     0       0.25
#> 10 host-tR…    10     6    1        0   0      0     0        0     0       0   
#> # ℹ 1,394 more rows
#> # ℹ 1 more variable: mean_qual <dbl>