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[*Back to home*](Home)
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*Previous: [Tertiary analysis](analysis/tertiary_analysis)*
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# The report file
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The report file is an html file which can be opened with a browser. It summarizes the results of the pipeline.
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## The samplesheet
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In the **Samples** section, the "display table" button enables to reveal the samplesheet used in the analysis.
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![samplesheet](../images/report/samplesheet.png)
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The table can be searched, filtered or ordered at will.
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## The FastQC summary
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The interactive graph in the **FastQC summary** section enables to see the total number of reads assigned to every sample in order to see the homogeneity between samples.
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![fastqc_summary](../images/report/fastqc.png)
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The points can be hovered in order to get the real values for each sample.
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## The MultiQC summary
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The **MultiQC summary** section is an iframe which embedes the MultiQC report of the output structure of the pipeline.
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![mutliqc](../images/report/multiqc.png)
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## The read distribution
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The **Read Distribution** section is an interactive graph presenting the results of the [well_summary](analysis/primary_analysis#expressionMatrix) file. Details for each sample can be seen by hovering the histogram bars of the plot.
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![readDistribution](../images/report/reads.png)
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## The genes detected
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The **Genes Detected** section enables to see the number of genes with at least one count for each sample.
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![genes_detected](../images/report/genes.png)
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## Sample filtering
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The **Sample filtering** section lets you know if samples have been filter out of the analysis because of their insufficient number of UMIs or detected genes.
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![genesDetected](../images/report/genesFound.png)
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## PCA and sample correlation heatmap
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The sections **PCA** and **Sample correlation** show the plots made in the [secondary analysis](analysis/secondary_analysis).
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![pca](../images/pca.png "PCA and heatmap of the correclation between samples")
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The link **View full PCA report** under the PCA enables to open the pdf file containing the distribution of the components as well as the plots of the other significative components.
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## Number of differentially expressed genes found
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The section "Number of differentially expressed genes found" enables to have a quick view of the number of genes found for every comparison. If many comparisons performed in the analysis, this table summarizes the genes found.
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![genesFound](../images/report/genesFound.png)
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## Comparisons
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For every comparison performed, a section is created giving the results of the comparisons. In every section and if differentially expressed genes (DEG) were detected, a MA-plot, a Volcano plot and a heatmap of the DEG can be found.
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![DE Analysis](../images/deAnalysis.png)
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The link **View clustering for all/comparison samples** located under the heatmap opens a pdf file containing both a heatmap with the samples of the comparison and a heatmap with all the samples of the project.
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In every comparison, the table of the DEG can also be opened with the **Display table** button of **DE genes table** section.
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The **Fonctionnal annotation enrichment** section as well as the **STRING DB** section enables to visualize gene ontology or kegg pathways enrichments and protein interactions for the DEG found in the comparison.
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![Tertiary Analysis](../images/terAnalysis.png)
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## Supplemental data
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The **Supplemental data** section enables to download files from the directory tree generated by the pipeline.
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![](../images/report/supplemental.png)
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## The tool versions
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At the end of the report, a table listing all the versions of the tools used in the pipeline enables reproducibility.
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![](../images/report/versions.png)
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<div align="right">
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<i>Next: <a href="outputs">The outputs</a></i>
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</div> |
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\ No newline at end of file |