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

Hide matching samples
Show only matching samples

Regex mode off

#### Export Plots

px
px
Aspect ratio
Plot scaling
X

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

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 1.0.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.

Report generated on 2024-11-28, 00:11 based on data in:

- `/app/data/results/fLkuRabeWWDwmlIgxa9TmFxWSP8LzEPOnHPEKOEk/results/star/SRR12535878`
- `/app/data/results/fLkuRabeWWDwmlIgxa9TmFxWSP8LzEPOnHPEKOEk/results/star/SRR14284493`
- `/app/data/results/fLkuRabeWWDwmlIgxa9TmFxWSP8LzEPOnHPEKOEk/results/cleaned`
- `/app/data/results/fLkuRabeWWDwmlIgxa9TmFxWSP8LzEPOnHPEKOEk/results/star/SRR14284494`
- `/app/data/results/fLkuRabeWWDwmlIgxa9TmFxWSP8LzEPOnHPEKOEk/results/read_composition_wo_filter`
- `/app/data/results/fLkuRabeWWDwmlIgxa9TmFxWSP8LzEPOnHPEKOEk/results/fastqc/cleaned`
- `/app/data/results/fLkuRabeWWDwmlIgxa9TmFxWSP8LzEPOnHPEKOEk/results/star/SRR12535752`

Welcome! Not sure where to start? Watch a tutorial video (6:06)

## General Statistics

Showing 4/4 rows and 9/10 columns.

Sample Name | % Assigned | M Assigned | % Aligned | M Aligned | % Trimmed | % Dups | % GC | Length | % Failed | M Seqs
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
SRR12535752 | 80.1% | 0.3 | 22.6% | 0.1 | 73.5% | 77.8% | 53% | 34 | 18% | 0.3
SRR12535878 | 58.9% | 0.4 | 21.9% | 0.1 | 68.5% | 91.1% | 52% | 34 | 18% | 0.5
SRR14284493 | 74.8% | 0.5 | 42.0% | 0.1 | 77.5% | 81.2% | 49% | 47 | 45% | 0.2
SRR14284494 | 75.1% | 0.3 | 26.5% | 0.1 | 78.2% | 65.7% | 50% | 38 | 27% | 0.2

#### General Statistics: Columns

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
--- | --- | --- | --- | --- | --- | ---
|| |  | featureCounts | % Assigned | % Assigned reads | `percent_assigned` | None
|| |  | featureCounts | M Assigned | Assigned reads (millions) | `Assigned` | read_count
|| |  | STAR | % Aligned | % Uniquely mapped reads | `uniquely_mapped_percent` | None
|| |  | STAR | M Aligned | Uniquely mapped reads (millions) | `uniquely_mapped` | read_count
|| |  | Cutadapt | % Trimmed | % Total Base Pairs trimmed | `percent_trimmed` | None
|| |  | FastQC | % Dups | % Duplicate Reads | `percent_duplicates` | None
|| |  | FastQC | % GC | Average % GC Content | `percent_gc` | None
|| |  | FastQC | Length | Average Sequence Length (bp) | `avg_sequence_length` | None
|| |  | FastQC | % Failed | Percentage of modules failed in FastQC report (includes those not plotted here) | `percent_fails` | None
|| |  | FastQC | M Seqs | Total Sequences (millions) | `total_sequences` | read_count

## featureCounts

Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

loading..

## STAR

STAR is an ultrafast universal RNA-seq aligner.

loading..

## Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.

loading..

## FastQC

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

### Sequence Quality Histograms

The mean quality value across each base position in the read. See the FastQC help.

loading..

### Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

loading..

### Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

Click a heatmap row to see a line plot for that dataset.

##### rollover for sample name

Position: -
%T: -
%C: -
%A: -
%G: -

### Per Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

loading..

### Per Base N Content

The percentage of base calls at each position for which an N was called. See the FastQC help.

loading..

### Sequence Length Distribution

The distribution of fragment sizes (read lengths) found. See the FastQC help.

loading..

### Sequence Duplication Levels

The relative level of duplication found for every sequence. See the FastQC help.

loading..

### Overrepresented sequences

The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

loading..

### Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

No samples found with any adapter contamination > 0.1%

### 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.