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The report file
The report file is an html file which can be opened with a browser. It summarizes the results of the pipeline.
The samplesheet
In the Samples section, the "display table" button enables to reveal the samplesheet used in the analysis.
The table can be searched, filtered or ordered at will.
The FastQC summary
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.
The points can be hovered in order to get the real values for each sample.
The MultiQC summary
The MultiQC summary section is an iframe which embedes the MultiQC report of the output structure of the pipeline.
The read distribution
The Read Distribution section is an interactive graph presenting the results of the well_summary file. Details for each sample can be seen by hovering the histogram bars of the plot.
The genes detected
The Genes Detected section enables to see the number of genes with at least one count for each sample.
Sample filtering
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.
PCA and sample correlation heatmap
The sections PCA and Sample correlation show the plots made in the secondary analysis.
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.
Number of differentially expressed genes found
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.
Comparisons
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.
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.
In every comparison, the table of the DEG can also be opened with the Display table button of DE genes table section.
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.
Supplemental data
The Supplemental data section enables to download files from the directory tree generated by the pipeline.
The tool versions
At the end of the report, a table listing all the versions of the tools used in the pipeline enables reproducibility.
Next: The outputs