Toolbox

### MultiQC Toolbox

####
Highlight Samples

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####
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

Hide matching samples
Show only matching samples

Regex mode off

#### Explain with AI

Configure AI settings to get explanations of plots and data in this report.

AI Provider

Endpoint

Use the OpenAI API-style requests with a custom endpoint.

Model

API Key

Keys entered here will be stored in your browser's local storage. See the docs.

Additional Payload

Any additional options passed in API request payload. Enter as a JSON object.

Context Window

The maximum number of tokens that can be processed in a single request

Anonymize samples off

#### Export Plots

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

Format:

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

##### Choose Plots

general_stats_table
star_summary_table
star_alignment_plot
star_gene_counts
table_scatter_plot

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

Settings are automatically saved. You can also save named configurations below.

#### Save Settings

You can save the toolbox settings for this report to the browser or as a file.

#### Load Settings

Choose a saved report profile from the browser or load from a file:

Load from File

#### Tool Citations

Please remember to cite the tools that you use in your analysis.

To help with this, you can download publication details of the tools mentioned in this report:

#### About MultiQC

This report was generated using MultiQC, version 1.30

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:

#

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

Loading report..
Report generated on 2025-11-25, 12:29 CET based on data in: `/mnt/fastcomputedata/acoudray/251126_crl_hepg2_new_genome/brbseq-nf-pipeline/work/d9/cfa574b4766946d54048e5b9e781ca`

Welcome! Not sure where to start? Watch a tutorial video (6:06)
Report AI Summary
Provider: , model: Chat with Seqera AI

## General Statistics

AI Summary
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Created with MultiQC
Showing 2/2 rows and 2/6 columns.

Sample Name | Total reads | Aligned | Aligned | Uniq aligned | Uniq aligned | Multimapped
--- | --- | --- | --- | --- | --- | ---
L030625CR01_01 | 457.3M | 346.8M | 75.8% | 346.8M | 75.8% | 0.0M
L030625CR02_01 | 385.5M | 300.0M | 77.8% | 300.0M | 77.8% | 0.0M

#### General Statistics: Columns

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 | Visible | Group | Column | Description | ID | Scale
--- | --- | --- | --- | --- | --- | ---
|| |  | STAR | Total reads | Number of input reads | `star-total_reads` | read_count
|| |  | STAR | Aligned | Mapped reads | `star-mapped` | read_count
|| |  | STAR | Aligned | % Mapped reads | `star-mapped_percent` |
|| |  | STAR | Uniq aligned | Uniquely mapped reads | `star-uniquely_mapped` | read_count
|| |  | STAR | Uniq aligned | % Uniquely mapped reads | `star-uniquely_mapped_percent` |
|| |  | STAR | Multimapped | Multiple mapped reads | `star-multimapped` | read_count

## STAR

Universal RNA-seq aligner.URL: https://github.com/alexdobin/STAR DOI: 10.1093/bioinformatics/bts635

### Summary Statistics

Summary statistics from the STAR alignment

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Created with MultiQC
Showing 2/2 rows and 10/19 columns.

Sample Name | Total reads | Aligned | Aligned | Uniq aligned | Uniq aligned | Multimapped | Avg. read len | Avg. mapped len | Splices | Annotated splices | GT/AG splices | GC/AG splices | AT/AC splices | Non-canonical splices | Mismatch rate | Del rate | Del len | Ins rate | Ins len
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
L030625CR01_01 | 457.3M | 346.8M | 75.8% | 346.8M | 75.8% | 0.0M | 99.0bp | 98.1bp | 100.9M | 99.6M | 99.9M | 0.4M | 0.0M | 0.6M | 0.4% | 0.0% | 1.4bp | 0.0% | 1.4bp
L030625CR02_01 | 385.5M | 300.0M | 77.8% | 300.0M | 77.8% | 0.0M | 98.0bp | 97.9bp | 103.0M | 101.8M | 102.2M | 0.4M | 0.0M | 0.5M | 0.4% | 0.0% | 1.6bp | 0.0% | 1.4bp

#### STAR: Summary Statistics: Columns

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

Sort | Visible | Group | Column | Description | ID | Scale
--- | --- | --- | --- | --- | --- | ---
|| |  |  | Total reads | Number of input reads | `star-total_reads` | read_count
|| |  |  | Aligned | Mapped reads | `star-mapped` | read_count
|| |  |  | Aligned | % Mapped reads | `star-mapped_percent` |
|| |  |  | Uniq aligned | Uniquely mapped reads | `star-uniquely_mapped` | read_count
|| |  |  | Uniq aligned | % Uniquely mapped reads | `star-uniquely_mapped_percent` |
|| |  |  | Multimapped | Multiple mapped reads | `star-multimapped` | read_count
|| |  |  | Avg. read len | Average input read length | `star-avg_input_read_length` |
|| |  |  | Avg. mapped len | Average mapped length | `star-avg_mapped_read_length` |
|| |  |  | Splices | Number of splices: Total | `star-num_splices` | read_count
|| |  |  | Annotated splices | Number of splices: Annotated (sjdb) | `star-num_annotated_splices` | read_count
|| |  |  | GT/AG splices | Number of splices: GT/AG | `star-num_GTAG_splices` | read_count
|| |  |  | GC/AG splices | Number of splices: GC/AG | `star-num_GCAG_splices` | read_count
|| |  |  | AT/AC splices | Number of splices: AT/AC | `star-num_ATAC_splices` | read_count
|| |  |  | Non-canonical splices | Number of splices: Non-canonical | `star-num_noncanonical_splices` | read_count
|| |  |  | Mismatch rate | Mismatch rate per base | `star-mismatch_rate` |
|| |  |  | Del rate | Deletion rate per base | `star-deletion_rate` |
|| |  |  | Del len | Deletion average length | `star-deletion_length` |
|| |  |  | Ins rate | Insertion rate per base | `star-insertion_rate` |
|| |  |  | Ins len | Insertion average length | `star-insertion_length` |

### Alignment Scores

AI Summary
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Created with MultiQC

### Gene Counts

Statistics from results generated using `--quantMode GeneCounts`. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

AI Summary
Provider: , model:
Chat with Seqera AI
Created with MultiQC

### Plot Table Data

Please select two table columns.

### Regex Help

Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.

    samp_1
    samp_1_edited
    samp_2
    samp_2_edited
    samp_3
    samp_3_edited
    prepended_samp_1
    tmp_samp_1_edited
    tmpp_samp_1_edited
    tmppp_samp_1_edited
    #samp_1_edited.tmp
    samp_11
    samp_11111

See regex101.com for a more heavy duty testing suite.