Generate QC Metrics

Computes quality control metrics from FASTQ and/or BAM files.

Usage

bb_qc(fastq_path = NULL, bam_path = NULL, use_fastqc = TRUE)

Arguments

fastq_path

Character or NULL. Path(s) to FASTQ file(s).

bam_path

Character or NULL. Path(s) to BAM file(s).

use_fastqc

Logical. Try to use system FastQC if available. Default TRUE.

Value

A bb_qc object containing:

read_counts

Total reads per file

quality_scores

Per-position quality score summary

gc_content

GC content distribution

read_lengths

Read length distribution

mapping_rate

Mapping rate from BAM files (if provided)

Examples

# \donttest{
# Create a test FASTQ
tmp <- tempfile(fileext = ".fastq")
writeLines(c(
  "@read1", "ACGTACGT", "+", "IIIIIIII",
  "@read2", "GCGCGCGC", "+", "HHHHHHHH"
), tmp)
qc <- bb_qc(fastq_path = tmp)
qc
#> bambamR QC Summary
#> ==================
#> Files analyzed: 1 
#>   file32931b85965d.fastq: 2 reads
# }