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If you use plots from MultiQC in a publication or presentation, please cite:

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 1.13

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

Sample Name	# total Sequences	# trimming discarded	% trimming discarded	# mapping to genes	% mapping to genes	# duplicate to genes	% duplicate to genes	# usable reads for genes	# mapping to genome	% mapping to genome	# duplicate to genome	% duplicate to genome	# usable reads for genome
mESCWT-rep1-input	965274	4025	0.42%	52073	5.39%	16422	31.54%	35651	870736	90.21%	212776	24.44%	657960
mESCWT-rep1-treated	970949	4540	0.47%	46279	4.77%	14238	30.77%	32041	877724	90.40%	221808	25.27%	655916
mESCWT-rep2-input	958658	4077	0.43%	47957	5.00%	15536	32.40%	32421	865690	90.30%	227494	26.28%	638196
mESCWT-rep2-treated	967068	4330	0.45%	46041	4.76%	14578	31.66%	31463	876088	90.59%	221399	25.27%	654689
mESCWT-rep3-input	962695	3449	0.36%	46907	4.87%	14187	30.24%	32720	875638	90.96%	212758	24.30%	662880
mESCWT-rep3-treated	971861	4583	0.47%	42576	4.38%	14421	33.87%	28155	883270	90.88%	252648	28.60%	630622

Sort	Group	Column	Description	ID	Scale
\|\|	Reads Stats	# total Sequences	Total number of raw reads sequenced for this sample	`total_sequences`	None
\|\|	Reads Stats	# trimming discarded	Number of discarded reads in trimming step (include adapter dimer, low QC, etc.)	`trimming_discarded_sequences`	None
\|\|	Reads Stats	% trimming discarded	Percentage of discarded reads in trimming step (include adapter dimer, low QC, etc.)	`trimming_discarded_percentage`	None
\|\|	Reads Stats	# mapping to genes	Number of reads that aligned into genes reference in mapping step	`mapping_to_genes_sequences`	None
\|\|	Reads Stats	% mapping to genes	Percentage of reads that aligned into genes reference in mapping step	`mapping_to_genes_percentage`	None
\|\|	Reads Stats	# duplicate to genes	Number of reads that aligned into genes reference after duplicate removal step	`duplicate_to_genes_sequences`	None
\|\|	Reads Stats	% duplicate to genes	Percentage of reads that aligned into genes reference after duplicate removal step	`duplicate_to_genes_percentage`	None
\|\|	Reads Stats	# usable reads for genes	Number of usable reads for detect modification in genes	`usable_to_genes_sequence`	None
\|\|	Reads Stats	# mapping to genome	Number of reads that aligned into genome reference in mapping step	`mapping_to_genome_sequences`	None
\|\|	Reads Stats	% mapping to genome	Percentage of reads that aligned into genome reference in mapping step	`mapping_to_genome_percentage`	None
\|\|	Reads Stats	# duplicate to genome	Number of reads that aligned into genome reference after duplicate removal step	`duplicate_to_genome_sequences`	None
\|\|	Reads Stats	% duplicate to genome	Percentage of reads that aligned into genome reference after duplicate removal step	`duplicate_to_genome_percentage`	None
\|\|	Reads Stats	# usable reads for genome	Number of usable reads for detect modification in genome	`usable_to_genome_sequence`	None

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