scRNAsequest Slide Deck

Introduction

This is a slide deck (part of scRNASequest pipeline).

This report contains basic QC plots generated by the pipeline. If you turn on the filter_step when running scAnalyzer, this report will also display QC plots before and after filtering.

Please go through the figures carefully and decide the cutoffs for data filtering.

QC plots

This section presents a series of QC plots.

These QC plots can be grouped into the following categories:

  • General QC

  • Q30 Bases Percentage

  • Reads Mapping Summary

General QC

The General QC plot section includes nine bar plots to visualize general metrics of the current single-cell project.

Estimated Number of Cells

Median UMI Counts per Cell

Median Genes per Cell

Number of Reads

Mean Reads per Cell

Total Genes Detected

Valid Barcodes%

Sequencing Saturation%

Fraction Reads in Cells%

Q30 Bases Percentage

The Q30 Bases Percentage includes three Q30 plots showing Barcode%, RNA Read% and UMI%.

Q30 Bases in Barcode%

Q30 Bases in RNA Read%

Q30 Bases in UMI%

Reads Mapping Summary

This Reads Mapping Summary section shows the percentage of reads mapped to different genomic features.

Genome%

Confidently to Genome%

Confidently to Intergenic Regions%

Confidently to Intronic Regions%

Confidently to Exonic Regions%

Confidently to Transcriptome%

Antisense to Gene%

Pre-filtering Plots

In this section, we present 8 pre-filtering figures. ## Counts and Genes

This plot shows Total Counts (X axis) v.s. Genes (Y axis) detected in each sample, before filtering.

Number of Genes

This plot shows Number of Genes (Y axis) detected in each sample, before filtering.

Top Genes

This plot shows Top Genes and % of Total Counts in each sample, before filtering.

Percentage of Top 50 Genes

This plot shows % of Total Counts of top 50 genes, before filtering.

Percentage of Top 100 Genes

This plot shows % of Total Counts of top 100 genes, before filtering.

Percentage of Top 200 Genes

This plot shows % of Total Counts of top 200 genes, before filtering.

Percentage of Top 500 Genes

This plot shows % of Total Counts of top 500 genes, before filtering.

Percentage of Mitochondria

This plot shows % of Mitochondria, before filtering.

Post-filtering Plots

Post-filtering plots can be used to examine the filtering cutoff.

This table summarizes number of cells and genes after each filtering step. The last row shows the final number after all steps.

Data filtering
Filter cutoff cell_number gene_number
MT 20 44419 31040
min cell 3 44419 25276
min gene 50 44419 25276
max gene 3000 31653 25276
max UMI 10000 31648 25276

Counts and Genes

This plot shows Total Counts (X axis) v.s. Genes (Y axis) detected in each sample, after filtering.

Number of Genes

This plot shows Number of Genes (Y axis) detected in each sample, after filtering.

Top Genes

This plot shows Top Genes and % of Total Counts in each sample, after filtering.

Percentage of Top 50 Genes

This plot shows % of Total Counts of top 50 genes, after filtering.

Percentage of Top 100 Genes

This plot shows % of Total Counts of top 100 genes, after filtering.

Percentage of Top 200 Genes

This plot shows % of Total Counts of top 200 genes, after filtering.

Percentage of Top 500 Genes

This plot shows % of Total Counts of top 500 genes, after filtering.

Percentage of Mitochondria

This plot shows % of Mitochondria, after filtering.