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.
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 |
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 |
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 |
Average Stats across barcodes | |
---|---|
No_of_Genes | 3,627 |
No_of_Transcripts | 3,721 |
Visualization of QC metrics before filtering
Helps determine the optimal number of principal components to retain for clustering & downstream analysis
Contribution of individual genes to principal components
Contribution of individual genes to principal components
## [1] "All the plots and the analysis shown henceforth is specific to single cell RNA-Seq"
## [1] "Error calculating Markers or calculation skipped based on number of clusters found!"
## NULL
## [1] "Isoform data analysis is skipped; --analyzeIsoformforReport = FALSE"