MoP4 - pipeline: MultiQC Report

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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 1.27.1

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/MultiQC/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

MultiQC is developed by:

MoP4 - pipeline

Please cite: Cozzuto L, Liu H, Pryszcz LP, Pulido TH, Delgado-Tejedor A, Ponomarenko J, Novoa EM. MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets. Front Genet. 2020 Mar 17;11:211. doi: 10.3389/fgene.2020.00211
And: Cozzuto L, Delgado-Tejedor A, Hermoso Pulido T, Novoa EM, Ponomarenko J. Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores. N. Methods Mol Biol. 2023;2624:185-205. doi: 10.1007/978-1-0716-2962-8_13.

Report generated on 2025-04-01, 17:14 UTC based on data in: /nfs/scratch01/bi/master_of_pores/98/7e30a12d4cb8dc12c41fa177a01313

Sample Name	Reads	Bases	Read N50	Longest Read	Shortest Read	Mean Length	Median Length	Mean Qual	Median Qual	Median length	Read N50	Median Qual	Median Identity	# Reads (K)	Total Bases (Mb)	Aligned Bases (Mb)
A	0.0M	3.3Mb	2463bp	5421bp	6bp	1616.0bp	2085	18.1	18.5	2156bp	2463bp	18.6	98.5%	2.0K	3.3Mb	3.3Mb
m6A	0.0M	3.0Mb	2201bp	6248bp	147bp	1496.0bp	1514	13.6	13.1	1511bp	2200bp	13.1	91.9%	2.0K	3.0Mb	3.0Mb

Sort	Group	Column	Description	ID	Scale
\|\|	nanoq	Reads	Number of reads	`nanoq-Number_of_reads`	read_count
\|\|	nanoq	Bases	Total bases sequenced	`nanoq-Number_of_bases`	base_count
\|\|	nanoq	Read N50	N50 read length	`nanoq-N50_read_length`
\|\|	nanoq	Longest Read	Longest read length	`nanoq-Longest_read`
\|\|	nanoq	Shortest Read	Shortest read length	`nanoq-Shortest_read`
\|\|	nanoq	Mean Length	Mean read length	`nanoq-Mean_read_length`
\|\|	nanoq	Median Length	Median read length (bp)	`nanoq-Median_read_length`
\|\|	nanoq	Mean Qual	Mean read quality (Phred scale)	`nanoq-Mean_read_quality`
\|\|	nanoq	Median Qual	Median read quality (Phred scale)	`nanoq-Median_read_quality`
\|\|	NanoStat	Median length	Median read length (bp) (Aligned)	`nanostat-nanostat_Median_read_length_aligned`	nucleotides
\|\|	NanoStat	Read N50	Read length N50 (Aligned)	`nanostat-nanostat_Read_length_N50_aligned`
\|\|	NanoStat	Median Qual	Median read quality (Phred scale) (Aligned)	`nanostat-nanostat_Median_read_quality_aligned`	phred_score
\|\|	NanoStat	Median Identity	Median percent identity (Aligned)	`nanostat-nanostat_Median_percent_identity_aligned`	percent_identity
\|\|	NanoStat	# Reads (K)	Number of reads (thousands) (Aligned)	`nanostat-nanostat_Number_of_reads_aligned`	long_read_count
\|\|	NanoStat	Total Bases (Mb)	Total bases (millions) (Aligned)	`nanostat-nanostat_Total_bases_aligned`	base_count
\|\|	NanoStat	Aligned Bases (Mb)	Total bases aligned (millions) (Aligned)	`nanostat-nanostat_Total_bases_aligned_aligned`	base_count

Alignment QC

Showing ²/₂ rows and ⁷/₇ columns.

File name	Mapped reads	Map %	Bases	Bases %	Avg read length	Max read length	identity
A_s.bam	2007	100.0%	3262038	99.1%	1639	5421	98.14%
m6A_s.bam	1999	100.0%	2946985	98.7%	1494	6248	91.40%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: alnQC-section-plot_table

Sort	Column	Description	ID
\|\|	Mapped reads	Mapped reads	`Mapped_reads`
\|\|	Map %	Map %	`Map`
\|\|	Bases	Bases	`Bases`
\|\|	Bases %	Bases %	`Bases-1`
\|\|	Avg read length	Avg read length	`Avg_read_length`
\|\|	Max read length	Max read length	`Max_read_length`
\|\|	identity	identity	`identity`

Assigned counts

Showing ²/₂ rows.

File name	Counts
A	2006
m6A	1994

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: Assigned_reads-section-plot_table

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Counts	Counts	`Counts`

nanoq

Reports read quality and length from nanopore sequencing data.URL: https://github.com/nerdna/nanoqDOI: 10.21105/joss.02991

Nanoq Summary

Statistics from Nanoq reports

Showing ²/₂ rows and ⁹/₉ columns.

Sample Name	Reads	Bases	Read N50	Longest Read	Shortest Read	Mean Length	Median Length	Mean Qual	Median Qual
A	0.0M	3.3Mb	2463bp	5421bp	6bp	1616.0bp	2085	18.1	18.5
m6A	0.0M	3.0Mb	2201bp	6248bp	147bp	1496.0bp	1514	13.6	13.1

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: nanoq_table_table

Sort	Column	Description	ID	Scale
\|\|	Reads	Number of reads	`Number_of_reads`	read_count
\|\|	Bases	Total bases sequenced	`Number_of_bases`	base_count
\|\|	Read N50	N50 read length	`N50_read_length`
\|\|	Longest Read	Longest read length	`Longest_read`
\|\|	Shortest Read	Shortest read length	`Shortest_read`
\|\|	Mean Length	Mean read length	`Mean_read_length`
\|\|	Median Length	Median read length (bp)	`Median_read_length`
\|\|	Mean Qual	Mean read quality (Phred scale)	`Mean_read_quality`
\|\|	Median Qual	Median read quality (Phred scale)	`Median_read_quality`

Read quality

Read counts categorised by read quality (Phred score).

Sequencing machines assign each generated read a quality score using the Phred scale. The phred score represents the liklelyhood that a given read contains errors. High quality reads have a high score.

Created with MultiQC

Read lengths

Read counts categorised by read length.

Created with MultiQC

v1.27.1

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Summary Statistics (Aligned)

Reads by quality

Sample Name	Median length	Mean length	Read N50	Median Qual	Mean Qual	Median Identity	Mean Identity	# Reads (K)	Total Bases (Mb)	Aligned Bases (Mb)
A	2156bp	1640bp	2463bp	18.6	18.3	98.5%	98.1%	2.0K	3.3Mb	3.3Mb
m6A	1511bp	1492bp	2200bp	13.1	13.6	91.9%	92.2%	2.0K	3.0Mb	3.0Mb

Sort	Column	Description	ID	Scale
\|\|	Median length	Median read length (bp)	`nanostat-Median_read_length_aligned`	nucleotides
\|\|	Mean length	Mean read length (bp)	`nanostat-Mean_read_length_aligned`	nucleotides
\|\|	Read N50	Read length N50	`nanostat-Read_length_N50_aligned`
\|\|	Median Qual	Median read quality (Phred scale)	`nanostat-Median_read_quality_aligned`	phred_score
\|\|	Mean Qual	Mean read quality (Phred scale)	`nanostat-Mean_read_quality_aligned`	phred_score
\|\|	Median Identity	Median percent identity	`nanostat-Median_percent_identity_aligned`	percent_identity
\|\|	Mean Identity	Average percent identity	`nanostat-Average_percent_identity_aligned`	percent_identity
\|\|	# Reads (K)	Number of reads (thousands)	`nanostat-Number_of_reads_aligned`	long_read_count
\|\|	Total Bases (Mb)	Total bases (millions)	`nanostat-Total_bases_aligned`	base_count
\|\|	Aligned Bases (Mb)	Total bases aligned (millions)	`nanostat-Total_bases_aligned_aligned`	base_count

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