Toolbox

MultiQC Toolbox

Highlight Samples

Regex mode off

Rename Samples

Click here for bulk input.

Paste two columns of a tab-delimited table here (eg. from Excel).

First column should be the old name, second column the new name.

Regex mode off

Show / Hide Samples

Regex mode off

Export Plots

Images
Data

Aspect ratio

Plot scaling

Download the raw data used to create the plots in this report below:

Format:

Note that additional data was saved in in2514_multiqc_report_data when this report was generated.

Choose Plots

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

Save Settings

You can save the toolbox settings for this report to the browser.

Load Settings

Choose a saved report profile from the dropdown box below:

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

RRBS Analysis Report for in2514

This report presents identified differential methylation cytosines (DMCs) and regions (DMRs).

JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like you have JavaScript disabled in your web browser. Please note that many of the report functions will not work as intended.

Differential Methylation

This section of the report presents identified differential methylation cytosines (DMCs) and regions (DMRs).

Workflow Description

A brief summary of the data workflow:

Data filtering: cytosines with read depth ≥ 5 in ≥ 2 samples in a group are kept, otherwise removed for that group before downstream analyses.
Detecting DMCs and DMRs: DMCs are detected with dss and DMRs are detected with dss. Significant DMCs and DMRs have FDR ≤ 0.05 (if P values are provided by statistical method) and absolute methylation difference ≥ 0.1.
Annotation of DMRs: each DMR is annotated by overlapping its genomic region with other functional regions, including genes, exons, introns, promoters, and CpG islands. The functional regions are derived from the ucsc database. The minimum size for an overlap is 1 bp.
Functional enrichment analyses of the overlapped genes: the overlapped genes identified in previous step are input into g:Profiler for functional enrichment analysis.
Plots: some plots such as heatmaps are generated to visualize the results.
Downloads: all result files are available for downloading at the Comparison Download section.

Sample Information

Here is a table of samples used for DMC/DMR analyses. The column group is used to group samples.

Showing ⁸/₈ rows and ²/₂ columns.

Sample Name	Comparision Group	Sample ID
line0	FFPE_NAT_Lung	FFPE_NAT_Lung_1
line1	FFPE_NAT_Lung	FFPE_NAT_Lung_2
line2	FFPE_Tumor_Lung	FFPE_Tumor_Lung_1
line3	FFPE_Tumor_Lung	FFPE_Tumor_Lung_2
line4	NAT_Liver	NAT_Liver_1
line5	NAT_Liver	NAT_Liver_2
line6	Tumor_Liver	Tumor_Liver_1
line7	Tumor_Liver	Tumor_Liver_2

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

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Comparision Group	The group name.	`group`	None
\|\|			Sample ID	The internal ID of the sample.	`sampleId`	None

Distribution of methylation values per sample

This figure displays the distribution of methylation values of all cytosines (or a sampled subset for the sake of performance) for each sample using violin plot.

Distribution of methylation values per group

This figure displays the distribution of methylation values averaged for each group using density plot. The number of cytosines (n) used is at the top.

Summary Table

The table below shows the number of DMCs identified for each comparison.

Showing ¹²/₁₂ rows and ⁹/₉ columns.

Sample Name	Type	Comparision Group	DMR Method	Input	StatOutput	Padj<=0.05	Padj<=0.05 & methDiff<=-0.1	Padj<=0.05 & methDiff>=0.1	File Name
line0_dmc	dmc	FFPE_NAT_Lung vs FFPE_Tumor_Lung	dss	2137683	92721	92583	46911	45672	dms_dss.FFPE_NAT_Lung_vs_FFPE_Tumor_Lung.tsv.gz
line0_dmr	dmr	FFPE_NAT_Lung vs FFPE_Tumor_Lung	dss	2137683	8731	NA	3526	5145	dmr_dss.FFPE_NAT_Lung_vs_FFPE_Tumor_Lung.tsv.gz
line1_dmc	dmc	FFPE_NAT_Lung vs NAT_Liver	dss	1839478	124013	123805	95837	27968	dms_dss.FFPE_NAT_Lung_vs_NAT_Liver.tsv.gz
line1_dmr	dmr	FFPE_NAT_Lung vs NAT_Liver	dss	1839478	12149	NA	9319	2708	dmr_dss.FFPE_NAT_Lung_vs_NAT_Liver.tsv.gz
line2_dmc	dmc	FFPE_NAT_Lung vs Tumor_Liver	dss	2076368	516635	516592	140130	376462	dms_dss.FFPE_NAT_Lung_vs_Tumor_Liver.tsv.gz
line2_dmr	dmr	FFPE_NAT_Lung vs Tumor_Liver	dss	2076368	43450	NA	9754	33333	dmr_dss.FFPE_NAT_Lung_vs_Tumor_Liver.tsv.gz
line3_dmc	dmc	FFPE_Tumor_Lung vs NAT_Liver	dss	1713499	182068	181948	124992	56956	dms_dss.FFPE_Tumor_Lung_vs_NAT_Liver.tsv.gz
line3_dmr	dmr	FFPE_Tumor_Lung vs NAT_Liver	dss	1713499	17166	NA	12886	4135	dmr_dss.FFPE_Tumor_Lung_vs_NAT_Liver.tsv.gz
line4_dmc	dmc	FFPE_Tumor_Lung vs Tumor_Liver	dss	1895689	448461	448428	121504	326924	dms_dss.FFPE_Tumor_Lung_vs_Tumor_Liver.tsv.gz
line4_dmr	dmr	FFPE_Tumor_Lung vs Tumor_Liver	dss	1895689	37686	NA	9167	28130	dmr_dss.FFPE_Tumor_Lung_vs_Tumor_Liver.tsv.gz
line5_dmc	dmc	NAT_Liver vs Tumor_Liver	dss	1951066	412645	412567	93558	319009	dms_dss.NAT_Liver_vs_Tumor_Liver.tsv.gz
line5_dmr	dmr	NAT_Liver vs Tumor_Liver	dss	1951066	32334	NA	4920	27316	dmr_dss.NAT_Liver_vs_Tumor_Liver.tsv.gz

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

Sort	Column	Description	ID	Scale
\|\|	Type	Type of differential methylation (region or cytosine)	`type`	None
\|\|	Comparision Group	The groups under comparison, separated by comma.	`cmp`	None
\|\|	DMR Method	The statistical method used.	`method`	None
\|\|	Input	The total number of cytosines fed into the statistical method.	`input`	None
\|\|	StatOutput	The total number of cytosine sites output by the statistical method; in most cases, this number equals to the number of significant sites; if not, the statistical method may filter out some sites such as non-significant ones.	`statOutput`	None
\|\|	Padj<=0.05	The number of significant sites.	`padj<=0.05`	None
\|\|	Padj<=0.05 & methDiff<=-0.1	The number of significant hypomethylated sites (former group is less methylated than latter). This is not applicable for comparisons involved more than 2 groups.	`padj<=0.05 & methDiff<=-0.1`	None
\|\|	Padj<=0.05 & methDiff>=0.1	The number of significant hypermethylated sites. For comparisons with > 2 groups, methDiff is computed as the difference between the maximum and minimum methylation values of all compared groups.	`padj<=0.05 & methDiff>=0.1`	None
\|\|	File Name	The source file of the summary	`file`	None

DMC Heatmap

Here are tab views of DMC comparison heatmaps.

DMR Heatmap

Here are tab views of DMR comparison heatmaps.

Functional Enrichment Table FFPE_NAT_Lung vs FFPE_Tumor_Lung

Showing ⁵⁰/₅₀ rows and ⁸/₈ columns.

Rank	Term Name	Query P-value	-log10(p-value)	Term Size	Query Size	Intersection Size	Term ID	Source
1	system development	1.114e-102	101.953	3985	2506	908	GO:0048731	GO:Biological Process
2	anatomical structure development	1.054e-101	100.977	5924	2506	1186	GO:0048856	GO:Biological Process
3	multicellular organism development	3.503e-100	99.456	4658	2506	1003	GO:0007275	GO:Biological Process
4	developmental process	2.236e-98	97.651	6478	2506	1253	GO:0032502	GO:Biological Process
5	multicellular organismal process	1.335e-94	93.875	7234	2506	1343	GO:0032501	GO:Biological Process
6	nervous system development	3.851e-88	87.414	2541	2506	646	GO:0007399	GO:Biological Process
7	anatomical structure morphogenesis	2.020e-82	81.695	2692	2506	659	GO:0009653	GO:Biological Process
8	neurogenesis	2.583e-64	63.588	1746	2506	460	GO:0022008	GO:Biological Process
9	cell differentiation	3.681e-64	63.434	4381	2506	872	GO:0030154	GO:Biological Process
10	cellular developmental process	4.145e-64	63.383	4382	2506	872	GO:0048869	GO:Biological Process
11	generation of neurons	2.976e-60	59.526	1517	2506	411	GO:0048699	GO:Biological Process
12	animal organ development	2.335e-56	55.632	3047	2506	653	GO:0048513	GO:Biological Process
13	biological regulation	1.369e-54	53.864	12671	2506	1870	GO:0065007	GO:Biological Process
14	neuron differentiation	6.933e-54	53.159	1434	2506	383	GO:0030182	GO:Biological Process
15	cell development	6.001e-53	52.222	2833	2506	611	GO:0048468	GO:Biological Process
16	regulation of biological process	1.952e-51	50.710	12278	2506	1817	GO:0050789	GO:Biological Process
17	cell communication	3.260e-48	47.487	6496	2506	1111	GO:0007154	GO:Biological Process
18	regulation of cell communication	3.580e-48	47.446	3453	2506	691	GO:0010646	GO:Biological Process
19	regulation of signaling	7.597e-48	47.119	3446	2506	689	GO:0023051	GO:Biological Process
20	signaling	2.001e-47	46.699	6471	2506	1105	GO:0023052	GO:Biological Process
21	cell adhesion	3.912e-44	43.408	1511	2506	375	GO:0007155	GO:Biological Process
22	regulation of cellular process	3.535e-43	42.452	11876	2506	1744	GO:0050794	GO:Biological Process
23	neuron development	1.140e-42	41.943	1170	2506	312	GO:0048666	GO:Biological Process
24	positive regulation of biological process	2.441e-42	41.612	6235	2506	1056	GO:0048518	GO:Biological Process
25	regulation of developmental process	3.274e-41	40.485	2453	2506	520	GO:0050793	GO:Biological Process
26	animal organ morphogenesis	7.159e-40	39.145	1037	2506	282	GO:0009887	GO:Biological Process
27	positive regulation of cellular process	7.194e-40	39.143	5886	2506	1001	GO:0048522	GO:Biological Process
28	signal transduction	6.761e-37	36.170	5979	2506	1002	GO:0007165	GO:Biological Process
29	neuron projection development	1.157e-36	35.937	1014	2506	271	GO:0031175	GO:Biological Process
30	regulation of signal transduction	4.175e-36	35.379	3020	2506	590	GO:0009966	GO:Biological Process
31	cell junction organization	8.946e-36	35.048	760	2506	222	GO:0034330	GO:Biological Process
32	cell morphogenesis	9.166e-36	35.038	986	2506	264	GO:0000902	GO:Biological Process
33	cell surface receptor signaling pathway	1.626e-35	34.789	2803	2506	556	GO:0007166	GO:Biological Process
34	tissue development	3.862e-35	34.413	2012	2506	434	GO:0009888	GO:Biological Process
35	regulation of biological quality	1.013e-34	33.994	2847	2506	560	GO:0065008	GO:Biological Process
36	plasma membrane bounded cell projection organization	1.164e-34	33.934	1572	2506	362	GO:0120036	GO:Biological Process
37	cell projection organization	1.651e-33	32.782	1615	2506	366	GO:0030030	GO:Biological Process
38	regulation of multicellular organismal process	3.341e-33	32.476	2928	2506	567	GO:0051239	GO:Biological Process
39	cellular response to stimulus	5.031e-33	32.298	7320	2506	1159	GO:0051716	GO:Biological Process
40	regulation of response to stimulus	2.970e-32	31.527	3958	2506	711	GO:0048583	GO:Biological Process
41	central nervous system development	4.849e-32	31.314	1038	2506	265	GO:0007417	GO:Biological Process
42	neuron projection morphogenesis	2.540e-30	29.595	654	2506	191	GO:0048812	GO:Biological Process
43	cell projection morphogenesis	2.601e-30	29.585	675	2506	195	GO:0048858	GO:Biological Process
44	plasma membrane bounded cell projection morphogenesis	8.725e-30	29.059	670	2506	193	GO:0120039	GO:Biological Process
45	synaptic signaling	1.034e-29	28.985	783	2506	214	GO:0099536	GO:Biological Process
46	trans-synaptic signaling	1.923e-29	28.716	759	2506	209	GO:0099537	GO:Biological Process
47	cell-cell signaling	2.130e-29	28.672	1316	2506	306	GO:0007267	GO:Biological Process
48	anterograde trans-synaptic signaling	1.509e-28	27.821	753	2506	206	GO:0098916	GO:Biological Process
49	chemical synaptic transmission	1.509e-28	27.821	753	2506	206	GO:0007268	GO:Biological Process
50	head development	2.871e-28	27.542	789	2506	212	GO:0060322	GO:Biological Process

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

Sort	Column	Description	ID	Scale
\|\|	Term Name	The short name used to describe this gene set.	`term_name`	None
\|\|	Query P-value	The hypergeometric p-value after correction for multiple testing.	`p_value`	None
\|\|	-log10(p-value)		`l10pv`	None
\|\|	Term Size	The number of genes that are annotated to this term.	`term_size`	None
\|\|	Query Size	The number of genes that were included in the query.	`query_size`	None
\|\|	Intersection Size	The number of genes in the input query that are annotated to the corresponding term.	`intersection_size`	None
\|\|	Term ID	The unique term identifier.	`term_id`	None
\|\|	Source	The database source for the term	`source`	None

Comparison Download

Showing ⁶/₆ rows and ³/₃ columns.

Sample Name	DMCs	DMRs	Functional Enrichment
FFPE_NAT_Lung_vs_FFPE_Tumor_Lung	Download	Download	Download
FFPE_NAT_Lung_vs_NAT_Liver	Download	Download	Download
FFPE_NAT_Lung_vs_Tumor_Liver	Download	Download	Download
FFPE_Tumor_Lung_vs_NAT_Liver	Download	Download	Download
FFPE_Tumor_Lung_vs_Tumor_Liver	Download	Download	Download
NAT_Liver_vs_Tumor_Liver	Download	Download	Download

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

Sort	Column	Description	ID	Scale
\|\|	DMCs	Identified DMCs.	`DMCs`	None
\|\|	DMRs	Identified DMRs.	`DMRs`	None
\|\|	Functional Enrichment	Functional enrichment of DMR overlapping genes.	`func`	None

Instructions to download all files

Click here to obtain the code to download all the files. We assume it is in your Download folder.

Find and open Terminal (Mac/Linux) or Windows Powershell (Windows).

Type cd ~/Download and Enter. If the code is downloaded to a different location, change ~/Download to the path to that folder.

Type bash download_links.ps1 (Mac/Linux) or Powershell.exe -ExecutionPolicy Bypass -File .\download_links.ps1 (Windows) and Enter.

Summary

Library Type: RRBS
Directionality: non-directional
Genome: hg19
Trimming: 5'R1: 0bp / 5'R2: 0bp / 3'R1: 0bp / 3'R2: 0bp / Illumina adapter / RRBS: On

Software Versions

Versions are collected at run time from the software output.

DSS: 2.46.0 ( R version: 4.2.3 )
nextflow: 23.10.1
pipeline: v2.3.3

Toggle navigation Powered by v1.11

RRBS Analysis Report for in2514

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

About MultiQC

RRBS Analysis Report for in2514

Differential Methylation

Workflow Description

Sample Information

Table Zwbd: Columns

Distribution of methylation values per sample

Distribution of methylation values per group

Summary Table

Table Zvkr: Columns

DMC Heatmap

DMR Heatmap

Functional Enrichment Table FFPE_NAT_Lung vs FFPE_Tumor_Lung

Table Msoh: Columns

Comparison Download

Table Ofzn: Columns

Instructions to download all files

Summary

Software Versions

Powered by

v1.11

Highlight Samples

Rename Samples

Show / Hide Samples