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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.11

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2026-08-21, 09:14 based on data in:

/projectnb/wax-dk/max/G260_G264_RNAseq/G264_vs_G221/SAMPLES
/projectnb/wax-dk/max/G260_G264_RNAseq/G264_vs_G221/Scripts/03_FASTQC
/projectnb/wax-dk/max/G260_G264_RNAseq/G264_vs_G221/Scripts/06_CollectMetrics

General Statistics

Showing ³⁷/₃₇ rows and ⁵/₆ columns.

Sample Name	M Reads	M Reads Mapped	% Assigned	M Assigned	% Aligned	M Aligned
G221_M69_G221_M69					63.5%	6.2
G221_M69_sorted			93.3%	5.8
G221_M69_statistics_for_all_accepted_reads	15.8	15.8
G221_M69_statistics_for_primary_reads	13.6	13.6
G221_M69_statistics_for_primary_unique_reads	12.4	12.4
G221_M70_G221_M70					63.9%	7.1
G221_M70_sorted			93.9%	6.7
G221_M70_statistics_for_all_accepted_reads	17.9	17.9
G221_M70_statistics_for_primary_reads	15.5	15.5
G221_M70_statistics_for_primary_unique_reads	14.3	14.3
G221_M71_G221_M71					64.4%	7.9
G221_M71_sorted			93.6%	7.4
G221_M71_statistics_for_all_accepted_reads	19.5	19.5
G221_M71_statistics_for_primary_reads	17.0	17.0
G221_M71_statistics_for_primary_unique_reads	15.7	15.7
G221_M72_G221_M72					55.5%	6.0
G221_M72_sorted			94.7%	5.7
G221_M72_statistics_for_all_accepted_reads	14.9	14.9
G221_M72_statistics_for_primary_reads	12.9	12.9
G221_M72_statistics_for_primary_unique_reads	12.0	12.0
G221_M73_G221_M73					70.2%	18.6
G221_M73_sorted			93.8%	17.4
G221_M73_statistics_for_all_accepted_reads	46.2	46.2
G221_M73_statistics_for_primary_reads	40.3	40.3
G221_M73_statistics_for_primary_unique_reads	37.1	37.1
G221_M74_G221_M74					72.0%	12.7
G221_M74_sorted			92.8%	11.8
G221_M74_statistics_for_all_accepted_reads	32.5	32.5
G221_M74_statistics_for_primary_reads	27.9	27.9
G221_M74_statistics_for_primary_unique_reads	25.4	25.4
G264_M01_sorted			93.7%	25.6
G264_M02_sorted			93.4%	20.5
G264_M03_sorted			91.7%	15.3
G264_M04_sorted			92.0%	14.5
G264_M05_sorted			92.6%	8.9
G264_M06_sorted			91.9%	13.6
statistics_for_primary_unique_reads	19.2	19.2

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Sort	Group	Column	Description	ID	Scale
\|\|	Samtools	M Reads	Total reads in the bam file (millions)	`flagstat_total`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	featureCounts	% Assigned	% Assigned reads	`percent_assigned`	None
\|\|	featureCounts	M Assigned	Assigned reads (millions)	`Assigned`	read_count
\|\|	STAR	% Aligned	% Uniquely mapped reads	`uniquely_mapped_percent`	None
\|\|	STAR	M Aligned	Uniquely mapped reads (millions)	`uniquely_mapped`	read_count

RSeQC

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

Infer experiment

Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

featureCounts

Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Samtools Flagstat

This module parses the output from samtools flagstat. All numbers in millions.

STAR

STAR is an ultrafast universal RNA-seq aligner.

Alignment Scores

Gene Counts

Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

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General Statistics

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RSeQC

Infer experiment

featureCounts

Samtools

Samtools Flagstat

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Alignment Scores

Gene Counts

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