Cogent™ NGS Discovery Software

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"