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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 1.15.dev0

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.

This report has been generated by the nf-core/checkatlas analysis pipeline. For information about how to interpret these results, please see the documentation.

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Report generated on 2023-07-22, 01:20 based on data in: /data/analysis/data_becavin/checkatlas_test/tuto/work/2a/2331793a40995f995033511fd51186

General Statistics

Showing ¹/₁ rows and ⁵/₈ columns.

Sample Name	Estimated Cells	Reads In Cells	Avg Reads/Cell	M Reads	Valid BC	Q30 BC	Q30 read	Q30 UMI
SC3pv3_GEX_Human_PBMC	5140	93.6%	35473	182.3	98.2%	96.8%	94.5%	96.1%

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

Sort	Group	Column	Description	ID	Scale
\|\|	Cell Ranger Count	Estimated Cells	Estimated Number of Cells	`estimated cells`	cell_count
\|\|	Cell Ranger Count	Reads In Cells	Fraction Reads in Cells	`reads in cells`	None
\|\|	Cell Ranger Count	Avg Reads/Cell	Mean Reads per Cell	`avg reads/cell`	reads_per_cell
\|\|	Cell Ranger Count	M Reads	Number of reads (millions)	`reads`	read_count
\|\|	Cell Ranger Count	Valid BC	Valid Barcodes	`valid bc`	None
\|\|	Cell Ranger Count	Q30 BC	Q30 Bases in Barcode	`Q30 bc`	None
\|\|	Cell Ranger Count	Q30 read	Q30 Bases in RNA Read	`Q30 read`	None
\|\|	Cell Ranger Count	Q30 UMI	Q30 Bases in UMI	`Q30 UMI`	None

Checkatlas Qc Report

Custom content with all qc plots found in your atlases

Checkatlas Umap Report

Custom content with all reductions plots found in your atlases

Checkatlas Tsne Report

Custom content with all reductions plots found in your atlases

CheckAtlas

CheckAtlas A one-liner tool for quality control of your single-cell atlases.

Atlas overview

Overview of your single-cell atlases

Showing ⁴/₄ rows and ⁷/₇ columns.

Sample Name	AtlasFileType	NbCells	NbGenes	AnnData.raw	AnnData.X	File_extension	File_path
pbmc_3k_multiome	Cellranger >= v3	3009.0	36601.0	False	True	pbmc_3k_multiome	/data/analysis/data_becavin/checkatlas_test/tuto/data5/pbmc_3k_multiome/outs/pbmc_unsorted_3k_filtered_feature_bc_matrix.h5
pbmc_5k_v3_v3	Cellranger >= v3	5025.0	33538.0	False	True	pbmc_5k_v3_v3	/data/analysis/data_becavin/checkatlas_test/tuto/data5/pbmc_5k_v3_v3/outs/5k_pbmc_v3_filtered_feature_bc_matrix.h5
pbmc_5k_v3_v7	Cellranger >= v3	5140.0	36601.0	False	True	pbmc_5k_v3_v7	/data/analysis/data_becavin/checkatlas_test/tuto/data5/pbmc_5k_v3_v7/outs/SC3pv3_GEX_Human_PBMC_filtered_feature_bc_matrix.h5
pbmc_6k_v1_v1	Cellranger < v3	5419.0	32738.0	False	True	pbmc_6k_v1_v1	/data/analysis/data_becavin/checkatlas_test/tuto/data5/pbmc_6k_v1_v1/outs/filtered_matrices_mex/hg19/matrix.mtx

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

Sort	Column	Description	ID	Scale
\|\|	AtlasFileType	AtlasFileType	`AtlasFileType`	None
\|\|	NbCells	NbCells	`NbCells`	None
\|\|	NbGenes	NbGenes	`NbGenes`	None
\|\|	AnnData.raw	AnnData.raw	`AnnData.raw`	None
\|\|	AnnData.X	AnnData.X	`AnnData.X`	None
\|\|	File_extension	File_extension	`File_extension`	None
\|\|	File_path	File_path	`File_path`	None

QC total_counts

QC of your atlases log10(Cellrank vs total-counts.

QC n_genes_by_counts

QC of your atlases log10(Cellrank vs n_genes_by_counts.

QC pct_counts_mt

QC of your atlases log10(Cellrank vs pct_counts_mt.

Classification metrics

Quality control metrics calculated on your atlases.

Showing ⁷/₇ rows and ²/₂ columns.

Sample Name	obs	davies_bouldin
pbmc_3k_multiome_cellranger_graphclust	cellranger_graphclust	1.1
pbmc_3k_multiome_cellranger_kmeans_5	cellranger_kmeans_5	0.4
pbmc_5k_v3_v3_cellranger_graphclust	cellranger_graphclust	0.7
pbmc_5k_v3_v3_cellranger_kmeans_10	cellranger_kmeans_10	0.6
pbmc_5k_v3_v7_cellranger_graphclust	cellranger_graphclust	1.5
pbmc_5k_v3_v7_cellranger_kmeans_10	cellranger_kmeans_10	1.0
pbmc_6k_v1_v1_cellranger_kmeans_10	cellranger_kmeans_10	1.0

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

Sort	Visible	Group	Column	Description	ID	Scale
\|\|		metric_cluster_table	obs	obs	`obs`	None
\|\|		metric_cluster_table	davies_bouldin	davies_bouldin	`davies_bouldin`	None

Annotation metrics

Quality control metrics calculated on your atlases.

Showing ³/₃ rows and ³/₃ columns.

Sample Name	Reference	obs	rand_index
pbmc_3k_multiome_cellranger_kmeans_5	cellranger_graphclust	cellranger_kmeans_5	0.5
pbmc_5k_v3_v3_cellranger_kmeans_10	cellranger_graphclust	cellranger_kmeans_10	0.9
pbmc_5k_v3_v7_cellranger_kmeans_10	cellranger_graphclust	cellranger_kmeans_10	0.6

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

Sort	Column	Description	ID	Scale
\|\|	Reference	Reference	`Reference`	None
\|\|	obs	obs	`obs`	None
\|\|	rand_index	rand_index	`rand_index`	None

Dimensionality reduction metrics

Quality control metrics calculated on your atlases.

Showing ¹⁰/₁₀ rows.

Sample Name	obsm
pbmc_3k_multiome_X_pca	X_pca
pbmc_3k_multiome_X_tsne	X_tsne
pbmc_3k_multiome_X_umap	X_umap
pbmc_5k_v3_v3_X_pca	X_pca
pbmc_5k_v3_v3_X_tsne	X_tsne
pbmc_5k_v3_v7_X_pca	X_pca
pbmc_5k_v3_v7_X_tsne	X_tsne
pbmc_5k_v3_v7_X_umap	X_umap
pbmc_6k_v1_v1_X_pca	X_pca
pbmc_6k_v1_v1_X_tsne	X_tsne

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

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			obsm	obsm	`obsm`	None

Atlas object explorer

Exploration of your Atlas object (Scanpy, Cellanger, Seurat)

Showing ⁴/₄ rows and ⁵/₅ columns.

Sample Name	atlas_obs	obsm	var
pbmc_3k_multiome	`cellranger_graphclust` `cellranger_kmeans_5`	`X_umap` `X_tsne` `X_pca`	`gene_ids` `feature_types` `genome`
pbmc_5k_v3_v3	`cellranger_graphclust` `cellranger_kmeans_10`	`X_tsne` `X_pca`	`gene_ids` `feature_types` `genome`
pbmc_5k_v3_v7	`cellranger_graphclust` `cellranger_kmeans_10`	`X_umap` `X_tsne` `X_pca`	`gene_ids` `feature_types` `genome`
pbmc_6k_v1_v1	`cellranger_kmeans_10`	`X_tsne` `X_pca`	`gene_ids`

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

Sort	Group	Column	Description	ID	Scale
\|\|	adata_table	atlas_obs	atlas_obs	`atlas_obs`	None
\|\|	adata_table	obsm	obsm	`obsm`	None
\|\|	adata_table	var	var	`var`	None
\|\|	adata_table	varm	varm	`varm`	None
\|\|	adata_table	uns	uns	`uns`	None

Cell Ranger

Cell Ranger Cell Ranger analyzes single cell expression or VDJ data produced by 10X Genomics.DOI: 10.1038/ncomms14049.

Count - Summary stats

Summary QC metrics from Cell Ranger count

Showing ¹/₁ rows and ⁹/₂₀ columns.

Sample Name	M Reads	Valid BC	Valid UMI	Saturation	Q30 BC	Q30 read	Q30 UMI	Estimated Cells	Reads In Cells	Avg Reads/Cell	Median UMI/Cell	Median Genes/Cell	Genes Detected	Reads Mapped	Confident Reads	Confident Intergenic	Confident Intronic	Confident Exonic	Confident Transcriptome	Reads Antisense
SC3pv3_GEX_Human_PBMC	182.3	98.2%	99.9%	60.9%	96.8%	94.5%	96.1%	5140	93.6%	35473	8685.0	2827.0	27572.0	95.9%	90.5%	3.6%	33.3%	53.6%	76.1%	10.1%

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

Sort	Group	Column	Description	ID	Scale
\|\|	Cell Ranger Count	M Reads	Number of reads (millions)	`reads`	None
\|\|	Cell Ranger Count	Valid BC	Valid Barcodes	`valid bc`	None
\|\|	Cell Ranger Count	Valid UMI	Valid UMIs	`valid umi`	None
\|\|	Cell Ranger Count	Saturation	Sequencing Saturation	`saturation`	None
\|\|	Cell Ranger Count	Q30 BC	Q30 Bases in Barcode	`Q30 bc`	None
\|\|	Cell Ranger Count	Q30 read	Q30 Bases in RNA Read	`Q30 read`	None
\|\|	Cell Ranger Count	Q30 UMI	Q30 Bases in UMI	`Q30 UMI`	None
\|\|	Cell Ranger Count	Estimated Cells	Estimated Number of Cells	`estimated cells`	cell_count
\|\|	Cell Ranger Count	Reads In Cells	Fraction Reads in Cells	`reads in cells`	None
\|\|	Cell Ranger Count	Avg Reads/Cell	Mean Reads per Cell	`avg reads/cell`	reads_per_cell
\|\|	Cell Ranger Count	Median UMI/Cell	Median UMI Counts per Cell	`median umi/cell`	None
\|\|	Cell Ranger Count	Median Genes/Cell	Median Genes per Cell	`median genes/cell`	None
\|\|	Cell Ranger Count	Genes Detected	Total Genes Detected	`genes detected`	None
\|\|	Cell Ranger Count	Reads Mapped	Reads Mapped to Genome	`reads mapped`	None
\|\|	Cell Ranger Count	Confident Reads	Reads Mapped Confidently to Genome	`confident reads`	None
\|\|	Cell Ranger Count	Confident Intergenic	Reads Mapped Confidently to Intergenic Regions	`confident intergenic`	None
\|\|	Cell Ranger Count	Confident Intronic	Reads Mapped Confidently to Intronic Regions	`confident intronic`	None
\|\|	Cell Ranger Count	Confident Exonic	Reads Mapped Confidently to Exonic Regions	`confident exonic`	None
\|\|	Cell Ranger Count	Confident Transcriptome	Reads Mapped Confidently to Transcriptome	`confident transcriptome`	None
\|\|	Cell Ranger Count	Reads Antisense	Reads Mapped Antisense to Gene	`reads antisense`	None

Count - BC rank plot

Barcode knee plot

The plot shows the count of filtered UMIs mapped to each barcode. Barcodes are not determined to be cell-associated strictly based on their UMI count. Instead, they could be determined based on their expression profile, or removed via Protein Aggregate Detection and Filtering and/or High Occupancy GEM Filtering. Therefore, some regions of the graph contain both cell-associated and background-associated barcodes. The color of the graph in these regions is based on the local density of barcodes that are cell-associated.

Count - Median genes

Median gene counts per cell

This plot shows the Median Genes per Cell as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point.

Count - Saturation plot

Sequencing saturation

This plot shows the Sequencing Saturation metric as a function of downsampled sequencing depth (measured in mean reads per cell), up to the observed sequencing depth. Sequencing Saturation is a measure of the observed library complexity, and approaches 1.0 (100%) when all converted mRNA transcripts have been sequenced. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point. The dotted line is drawn at a value reasonably approximating the saturation point.

nf-core/checkatlas Methods Description

Suggested text and references to use when describing pipeline usage within the methods section of a publication.

Methods

Data was processed using nf-core/checkatlas v1.0dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v23.04.1 (Di Tommaso et al., 2017) with the following command:

nextflow run nf-core-checkatlas -r dev --path /data/analysis/data_becavin/checkatlas_test/tuto/data5/

References

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192

Notes:

If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

nf-core/checkatlas Software Versions

are collected at run time from the software output.

Process Name	Software	Version
`CUSTOM_DUMPSOFTWAREVERSIONS`	`python`	`3.10.12`
	`yaml`	`6.0.1`
`LIST_CELLRANGER_ATLASES`	`checkatlas`	`0.3.9`
`LIST_SCANPY_ATLASES`	`checkatlas`	`0.3.9`
`LIST_SEURAT_ATLASES`	`checkatlas`	`0.3.9`
`Workflow`	`Nextflow`	`23.04.1`
	`nf-core/checkatlas`	`1.0dev`

nf-core/checkatlas Workflow Summary

- this information is collected when the pipeline is started.

Core Nextflow options

revision: dev
runName: zen_lavoisier
launchDir: /data/analysis/data_becavin/checkatlas_test/tuto
workDir: /data/analysis/data_becavin/checkatlas_test/tuto/work
projectDir: /home/becavin/.nextflow/assets/becavin-lab/nf-core-checkatlas
userName: becavin
profile: standard
configFiles: N/A

Input/output options

path: /data/analysis/data_becavin/checkatlas_test/tuto/data5/
outdir: N/A

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General Statistics

General Statistics: Columns

Checkatlas Qc Report

Checkatlas Umap Report

Checkatlas Tsne Report

CheckAtlas

Atlas overview

Table Cgya: Columns

QC total_counts

QC n_genes_by_counts

QC pct_counts_mt

Classification metrics

Table Bwxa: Columns

Annotation metrics

Table Ubfv: Columns

Dimensionality reduction metrics

Table Upgm: Columns

Atlas object explorer

Table Vmup: Columns

Cell Ranger

Count - Summary stats

Table Wyjk: Columns

Count - BC rank plot Help

Count - Median genes Help

Count - Saturation plot Help

nf-core/checkatlas Methods Description

Methods

References

Notes:

nf-core/checkatlas Software Versions

nf-core/checkatlas Workflow Summary

v1.15.dev0

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Count - BC rank plot

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Count - Saturation plot