summary_stats_fastp: Get read quality summary statistics from fastp

In almeidasilvaf/GEAtlas: Building Expression Atlas from RNA-Seq data

Get read quality summary statistics from fastp

Description

Get read quality summary statistics from fastp

Usage

summary_stats_fastp(fastp_qcdir = "results/QC_dir/fastp_stats")

Arguments

fastp_qcdir

Character with path to the directory where .json files from fastp are stored. Default: results/QC_dir/fastp_stats.

Value

A data frame of fastp summary stats for each sample with the following variables:

• Sample

• sequencing

• before_nreads

• before_nbases

• before_q20bases

• before_q30bases

• before_q20rate

• before_q30rate

• before_GCcontent

• before_meanlength

• after_nreads

• after_nbases

• after_q20bases

• after_q30bases

• after_q20rate

• after_q30rate

• after_GCcontent

• after_meanlength

• filter_n_passed

• filter_n_lowquality

• filter_n_too_many_N

• filter_n_tooshort

• filter_n_toolong

• duplication_rate

Examples

fastp_qcdir <- system.file("extdata", package = "bears")
fastp_stats <- summary_stats_fastp(fastp_qcdir)

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.