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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 1.25.2

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.

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Report generated on 2025-01-20, 19:33 UTC based on data in: /nfs/scratch02/enovoa/ntodorov/nextflowwork/P2_RNA241107_Diet12i2_Lvr_mRNA_F0/nfs/scratch02/enovoa/ntodorov/nextflowwork/P2_RNA15052024_LiverSequencing_F0/WORK_MOP4_v012025_dor510_pseU/82/b674932110a9194d5308127c0dc871

General Statistics

Showing ⁰/₆ rows and ³/₉ columns.

Sample Name	Reads	Bases	Read N50	Longest Read	Shortest Read	Mean Length	Median Length	Mean Qual	Median Qual
pod5---bc_23	0.0M	18.0Mb	1366bp	9126bp	34bp	1038.0bp	873	18.0	18.4
pod5---bc_48	0.0M	24.7Mb	1210bp	19320bp	13bp	943.0bp	822	17.8	18.4
pod5---bc_101	0.0M	25.3Mb	1351bp	87934bp	28bp	1004.0bp	844	17.8	18.3
pod5---bc_102	0.0M	20.6Mb	1586bp	14125bp	73bp	1212.0bp	934	18.2	18.7
pod5---bc_103	0.0M	25.1Mb	1494bp	10226bp	31bp	1146.0bp	888	18.0	18.5
pod5---bc_104	0.0M	21.5Mb	1528bp	13731bp	19bp	1149.0bp	904	18.0	18.5

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

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`

Alignment QC

Showing ⁰/₆ rows and ⁷/₇ columns.

File name	Mapped reads	Map %	Bases	Bases %	Avg read length	Max read length	identity
pod5---bc_23_s.bam	17140	100.0%	17538382	97.8%	1046	9126	97.51%
pod5---bc_48_s.bam	25864	100.0%	24073480	97.6%	953.0	19320	97.30%
pod5---bc_101_s.bam	24874	100.0%	24640480	97.6%	1014	87934	97.24%
pod5---bc_102_s.bam	16867	100.0%	20110902	97.9%	1217	14125	97.29%
pod5---bc_103_s.bam	21687	100.0%	24536741	98.1%	1153	10226	97.22%
pod5---bc_104_s.bam	18525	100.0%	20971562	97.9%	1156	13731	97.23%

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 ⁰/₆ rows.

File name	Counts
pod5---bc_23	15199.0
pod5---bc_48	23234.0
pod5---bc_101	22471.0
pod5---bc_102	14972.0
pod5---bc_103	19514.0
pod5---bc_104	16441.0

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 ⁰/₆ rows and ⁹/₉ columns.

Sample Name	Reads	Bases	Read N50	Longest Read	Shortest Read	Mean Length	Median Length	Mean Qual	Median Qual
pod5---bc_23	0.0M	18.0Mb	1366bp	9126bp	34bp	1038.0bp	873	18.0	18.4
pod5---bc_48	0.0M	24.7Mb	1210bp	19320bp	13bp	943.0bp	822	17.8	18.4
pod5---bc_101	0.0M	25.3Mb	1351bp	87934bp	28bp	1004.0bp	844	17.8	18.3
pod5---bc_102	0.0M	20.6Mb	1586bp	14125bp	73bp	1212.0bp	934	18.2	18.7
pod5---bc_103	0.0M	25.1Mb	1494bp	10226bp	31bp	1146.0bp	888	18.0	18.5
pod5---bc_104	0.0M	21.5Mb	1528bp	13731bp	19bp	1149.0bp	904	18.0	18.5

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

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