QCreport: A post Alignment quality control of reads

In ORFik: Open Reading Frames in Genomics

Description

The ORFik QC uses the aligned files (usually bam files), fastp and STAR log files combined with annotation to create relevant statistics.

This report consists of several steps:
1. Convert bam file / Input files to ".ofst" format, if not already done. This format is around 400x faster to use in R than the bam format.
2. From this report you will get a summary csv table, with distribution of aligned reads and overlap counts over transcript regions like: leader, cds, trailer, lincRNAs, tRNAs, rRNAs, snoRNAs etc. It will be called STATS.csv. And can be imported with QCstats function.
3. It will also make correlation plots and meta coverage plots, so you get a good understanding of how good the quality of your NGS data production + aligner step were.
4. Count tables are produced, similar to HTseq count tables. Over mrna, leader, cds and trailer separately. This tables are stored as SummarizedExperiment, for easy loading into DEseq, conversion to normalized fpkm values, or collapsing replicates in an experiment. And can be imported with countTable function.
Everything will be outputed in the directory of your NGS data, inside the folder ./QC_STATS/, relative to data location in 'df'. You can specify new out location with out.dir if you want.
To make a ORFik experiment, see ?ORFik::experiment
To see some normal mrna coverage profiles of different RNA-seq protocols: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310221/figure/F6/

Usage

QCreport(df, out.dir = dirname(df$filepath[1]), BPPARAM = bpparam())

Arguments

df	an ORFik experiment
out.dir	optional output directory, default: dirname(df$filepath[1]). Will make a folder called "QC_STATS" with all results in this directory.
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers

Value

invisible(NULL) (objects are stored to disc)

See Also

Other QC report: QCplots(), QCstats()

Examples

# Load an experiment
df <- ORFik.template.experiment()
# Run QC
# QCreport(df)

ORFik documentation built on March 27, 2021, 6 p.m.