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FastQC-viz: FastQC parser

Source: R/parse_fastqc.R
parse_fastqc.Rd

Reads the raw fastqc_data.txt file and create a list with all of the modules. Each module contains a list with content and status.

Usage

parse_fastqc(fastq_data_file)

Arguments

fastq_data_file

Path for the fastqc_data.txt

Value

list, each module has content and status.

Details

These are the modules:

  • "basic_statistics"

  • "per_base_sequence_quality"

  • "per_sequence_quality_scores"

  • "per_base_sequence_content"

  • "per_sequence_gc_content"

  • "per_base_n_content"

  • "sequence_length_distribution"

  • "sequence_duplication_levels"

  • "overrepresented_sequences"

  • "adapter_content"

  • "comments"

Examples

fastqc_data <- parse_fastqc(system.file("extdata", "SRR622457_2_fastqc.txt", package = "fastqcviz"))
fastqc_data$overrepresented_sequences
#> $content
#> # A tibble: 1 × 4
#>   sequence                                      count percentage possible_source
#>   <chr>                                         <chr> <chr>      <chr>          
#> 1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN… 15290 0.6116     No Hit         
#> 
#> $status
#> [1] "warn"
#>