load_paired_end_qc_data: Load QC metrics data from paired-end RNA-seq processing

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Load QC metrics data from paired-end RNA-seq processing

Description

Load QC data files generated by MultiQC for various stages of paired-end RNA-seq data processing using the automated RNA-seq data processing WDL workflow.

Usage

load_paired_end_qc_data(data_dir)

Arguments

data_dir

A string denoting the local path where all the data files are stored.

Details

The automated RNA-seq data processing workflow produces several tables with various metrics. Additionally, several tables can be exported from the MultiQC HTML report. This function will import all of these data into a list for further processing in R. The assumed data files are

• multiqc_fastqc.txt: An auto-generated workflow file with general FASTQC statistics.

• multiqc_hisat2.txt: An auto-generated workflow file with HISAT2 alignment statistics.

• multiqc_rseqc_bam_stat.txt: An auto-generated workflow file with alignment statistics generated by RSeQC.

• multiqc_rseqc_read_distribution.txt: An auto-generated workflow file with alignment categorizations to different types of genomic regions (introns, exons, integenic, etc.).

• multiqc_salmon.txt: An auto-generated workflow file with mapping statistics from Salmon.

• multiqc_trimmomatic.txt: An auto-generated workflow file with trimming and read quality filtering statistics using Trimmomatic.

• rseqc_inner_distance_plot.tsv: Table exported from the MultiQC HTML report with inner distance statistics between pairs of reads.

• salmon_plot.tsv: Table exported from the MultiQC HTML report with RNA fragment length distribution statistics as estimated by Salmon.

• fastqc_per_base_sequence_quality_plot.tsv: Table exported from the MultiQC HTML report with per base PHRED scores statistics generated by FASTQC.

• fastqc_per_sequence_quality_scores_plot.tsv: Table exported from the MultiQC HTML report with per sequence PHRED score statistics generated by FASTQC.

• fastqc_per_sequence_gc_content_plot.tsv: Table exported from the MultiQC HTML report with per sequence GC content statistics generated by FASTQC.

• fastqc_sequence_duplication_levels_plot.tsv: Table exported from the MultiQC HTML report with sequence duplication statistics generated by FASTQC.

• fastqc_adapter_content_plot.tsv: Table exported from the MultiQC HTML report with adapter content statistics generated by FASTQC.

• rseqc_known_junction_saturation_plot.tsv: Table exported from the MultiQC HTML report with junction saturation statistics for known splice junctions.

• rseqc_novel_junction_saturation_plot.tsv: Table exported from the MultiQC HTML report with junction saturation statistics for novel splice junctions.

Value

A list with several elements:

• fastqc: Data frame imported from multiqc_fastqc.txt.

• hisat2: Data frame imported from multiqc_hisat2.txt.

• rseqc_bam: Data frame imported from multiqc_rseqc_bam_stat.txt.

• rseqc_alignment_category: Data frame imported from multiqc_rseqc_read_distribution.txt.

• salmon: Data frame imported from multiqc_salmon.txt.

• trimmomatic: Data frame imported from multiqc_trimmomatic.txt.

• inner_dist: Data frame imported from rseqc_inner_distance_plot.tsv.

• frag_length: Data frame imported from salmon_plot.tsv.

• phred_bp: Data frame imported from fastqc_per_base_sequence_quality_plot.tsv.

• phred_seq: Data frame imported from fastqc_per_sequence_quality_scores_plot.tsv.

• gc_content: Data frame imported from fastqc_per_sequence_gc_content_plot.tsv.

• seq_duplication: Data frame imported from fastqc_sequence_duplication_levels_plot.tsv.

• adapter_content: Data frame imported from fastqc_adapter_content_plot.tsv.

• known_junction: Data frame imported from rseqc_known_junction_saturation_plot.tsv.

• novel_junction: Data frame imported from rseqc_novel_junction_saturation_plot.tsv.

bryancquach/omixjutsu documentation built on Jan. 29, 2023, 3:47 p.m.