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Important Note:

This is a preliminary report based on default settings and parameters. Please use CogentDS v2.1 for in-depth and advanced analysis. Ambient RNA decontamination and QC are skipped for preliminary reporting.

For Bulk-RNA data sets, this report is not optimized and provides analysis specific to single cell RNA sequencing. Please use CogentDS v2.1 (Bulk RNA app) for in-depth analysis and interpretation for Bulk RNA sequencing data sets.


Experimental Overview

Read Stats

Total Counts % (of Barcoded Reads) % (of Trimmed Reads)
Barcoded_Reads 90,000 100.00 NA
Trimmed_Reads 88,895 98.77 100
Unmapped_Reads 2,364 2.63 2.66
Mapped_Reads 84,209 93.57 94.73
Uniquely_Mapped_Reads 78,670 87.41 88.5
Multimapped_Reads 5,539 6.15 6.23
Chimeric_Reads 2,003 2.23 2.25
Ribosomal_Reads 2,294 2.55 2.58
Mitochondrial_Reads 12,423 13.80 13.97
Usable 69,492 77.21 78.17
Undesirable 14,717 16.35 16.56

Gene Body Assignment Breakdown

Total Counts % (of Mapped Reads)
Mapped_Reads 84,209 100.00
Exon_Reads 70,689 83.94
Intron_Reads 6,093 7.24
Gene_Reads 76,782 91.18
Intergenic_Reads 7,427 8.82

Undesirable Read Breakdown

Total Counts % (of Mapped Reads)
Mapped_Reads 84,209 100.00
Ribosomal_Reads 2,294 2.72
Mitochondrial_Reads 12,423 14.75
Usable 69,492 82.52

Other Stats

Average Stats across barcodes
No_of_Genes 3,627
No_of_Transcripts 3,721

Data Statistics Plot


QC Analysis

QC Plots

Visualization of QC metrics before filtering


Principal Component Analysis (PCA)

Elbow Plot

Helps determine the optimal number of principal components to retain for clustering & downstream analysis


Gene Loadings

Contribution of individual genes to principal components


Gene Loadings across First 5 PCs

Contribution of individual genes to principal components


Principal Component Analysis (PCA) Plot for 1:5 components


Uniform Manifold Approximation Projection (UMAP Plot)

## [1] "All the plots and the analysis shown henceforth is specific to single cell RNA-Seq"


Differential Gene Markers across clusters

Differential Marker Gene Expression Heatmap

## [1] "Error calculating Markers or calculation skipped based on number of clusters found!"

Differential Marker Gene Table

## NULL

Isoform Analysis

## [1] "Isoform data analysis is skipped; --analyzeIsoformforReport = FALSE"

Displaying Isoform Based UMAP seurat clusters

Displaying Isoform Based UMAP Gene based seurat clusters


Differential Isoform Markers across clusters

Differential Isoform Markers Expression Heatmap


Differential Isoform Markers Table