Library preparation and sequencing data analysis report
Project name (ID): SIT-AGDS_DS384_Huh7_TGFb_SB_MOA
Overview
Library preparation summary
Library name
Number of samples
AGDS_DS384_Huh7_TGFb_SB_MOA_01
384
AGDS_DS384_Huh7_TGFb_SB_MOA_02
384
Library sequencing summary
PASSWARNING
Library? FASTQ name of the BRB-seq library
PF_reads? The total number of reads
Avg. nb. reads/sample? Defined as the number of demultiplexed reads / used samples
q30 R1? Rate of bases in Read 1 (BC+UMI) with Q >= 30
q30 R2? Rate of bases in Read 2 (genomic) with Q >= 30
AGDS_DS384_Huh7_TGFb_SB_MOA_01
475696847
1,174,652
0.958451
0.936529
AGDS_DS384_Huh7_TGFb_SB_MOA_02
354544440
876,190.9
0.957707
0.931497
Library alignment summary
PASSWARNING
Library? FASTQ name of the BRB-seq library
Genome assembly? Reference genome used for alignment
Nb. Mapped? Total number of reads mapped against the genome
% Mapped? % of the reads mapped against the genome
Nb. Mapped to exons? Total number of quantified reads
% Exons? Total % of quantified counts
Nb. genes? Average number of detected genes across used samples
Nb. ERCC? Total number of reads mapped to ERCC spike-ins
% ERCC? Total % of reads mapped to ERCC spike-ins
AGDS_DS384_Huh7_TGFb_SB_MOA_01
homo_sapiens GRCh38 114
315,846,367
70.02
267,678,491
59.34
12564.39
49,168,563
11.95
AGDS_DS384_Huh7_TGFb_SB_MOA_02
homo_sapiens GRCh38 114
273,346,265
81.24
218,804,759
65.03
12264.34
30,523,956
12.24
AGDS_DS384_Huh7_TGFb_SB_MOA_01
Number of sequencing reads, per sample - AGDS_DS384_Huh7_TGFb_SB_MOA_01? Per sample identification statistics, presented in barplot and plate view. The order of samples in barplot can be changed to default, row-wise and column-wise.
Hover for detailed sample information.
Number of RNA spike-ins reads, per sample - AGDS_DS384_Huh7_TGFb_SB_MOA_01? Per-sample ERCC (RNA spike-in) statistics are displayed in both bar plot and plate view. The sample order in the bar plot can be adjusted to default, row-wise, or column-wise.
Hover for detailed sample information.
Spike-ins concentration ? This plot shows the theoretical ERCC concentrations from the Thermo Fisher Scientific Mix 1 spike-in list, alongside the observed ERCC expression levels, enabling a comparison between expected and actual RNA spike-in performance.
Spike-ins identification ? This plot compares the number of reads per sample with the percentage of identified ERCC, showing both theoretical and observed traces. The theoretical ERCC percentage is calculated by averaging ERCC counts across samples and dividing this constant by each sample’s sequencing depth, then multiplying by 100%.
Sample identification compared to spike-ins ? The plot shows the comparison of variability between total reads per sample and identified spike-ins, where lower ERCC variability suggests minimal technical noise.
Spike-ins clisters ? The PCA plot clusters samples based on normalized ERCC expression values. Samples that cluster closely together exhibit similar ERCC expression, suggesting consistent technical performance across those samples.
Alignment statistics, per sample - AGDS_DS384_Huh7_TGFb_SB_MOA_01? Per sample total alignment statistics perfomed by STARsolo, presented in barplot and plate view. The order of samples in barplot can be changed to default, row-wise and column-wise.
Hover for detailed sample information.
Number of detected genes, per sample - AGDS_DS384_Huh7_TGFb_SB_MOA_01? Per sample gene detection statistics, presented in barplot and plate view. The order of samples in barplot can be changed to default, row-wise and column-wise.
Hover for detailed sample information.
Compare sample-wise statistics - AGDS_DS384_Huh7_TGFb_SB_MOA_01? This scatter plot enables comparison of various individual statistics, such as the number of reads, genes, alignment percentage, and ERCC counts per sample. Both the x and y axes can be customized using drop-down menus to explore relationships between these metrics.
Hover for detailed sample information.
Principle Component Analysis - AGDS_DS384_Huh7_TGFb_SB_MOA_01? The PCA plot displays the general expression profiles of all samples, with dots sized according to read counts. It helps identify patterns and clusters in gene expression, showing how samples with similar or differing profiles group together based on their overall expression patterns.
This plot was generated using truncated PCA (irlba).
Hover for detailed sample information.
Top-10 most expressed genes across samples - AGDS_DS384_Huh7_TGFb_SB_MOA_01? The pie chart shows the top 10 most highly expressed genes, with each slice representing their percentage of total gene expression.
Hover for detailed sample information.
Top-10 most expressed biotypes across samples - AGDS_DS384_Huh7_TGFb_SB_MOA_01? The pie chart shows the top 10 most highly expressed gene biotypes, with each slice representing their percentage of total gene expression.
Hover for detailed sample information.
AGDS_DS384_Huh7_TGFb_SB_MOA_02
Number of sequencing reads, per sample - AGDS_DS384_Huh7_TGFb_SB_MOA_02? Per sample identification statistics, presented in barplot and plate view. The order of samples in barplot can be changed to default, row-wise and column-wise.
Hover for detailed sample information.
Number of RNA spike-ins reads, per sample - AGDS_DS384_Huh7_TGFb_SB_MOA_02? Per-sample ERCC (RNA spike-in) statistics are displayed in both bar plot and plate view. The sample order in the bar plot can be adjusted to default, row-wise, or column-wise.
Hover for detailed sample information.
Spike-ins concentration ? This plot shows the theoretical ERCC concentrations from the Thermo Fisher Scientific Mix 1 spike-in list, alongside the observed ERCC expression levels, enabling a comparison between expected and actual RNA spike-in performance.
Spike-ins identification ? This plot compares the number of reads per sample with the percentage of identified ERCC, showing both theoretical and observed traces. The theoretical ERCC percentage is calculated by averaging ERCC counts across samples and dividing this constant by each sample’s sequencing depth, then multiplying by 100%.
Sample identification compared to spike-ins ? The plot shows the comparison of variability between total reads per sample and identified spike-ins, where lower ERCC variability suggests minimal technical noise.
Spike-ins clisters ? The PCA plot clusters samples based on normalized ERCC expression values. Samples that cluster closely together exhibit similar ERCC expression, suggesting consistent technical performance across those samples.
Alignment statistics, per sample - AGDS_DS384_Huh7_TGFb_SB_MOA_02? Per sample total alignment statistics perfomed by STARsolo, presented in barplot and plate view. The order of samples in barplot can be changed to default, row-wise and column-wise.
Hover for detailed sample information.
Number of detected genes, per sample - AGDS_DS384_Huh7_TGFb_SB_MOA_02? Per sample gene detection statistics, presented in barplot and plate view. The order of samples in barplot can be changed to default, row-wise and column-wise.
Hover for detailed sample information.
Compare sample-wise statistics - AGDS_DS384_Huh7_TGFb_SB_MOA_02? This scatter plot enables comparison of various individual statistics, such as the number of reads, genes, alignment percentage, and ERCC counts per sample. Both the x and y axes can be customized using drop-down menus to explore relationships between these metrics.
Hover for detailed sample information.
Principle Component Analysis - AGDS_DS384_Huh7_TGFb_SB_MOA_02? The PCA plot displays the general expression profiles of all samples, with dots sized according to read counts. It helps identify patterns and clusters in gene expression, showing how samples with similar or differing profiles group together based on their overall expression patterns.
This plot was generated using truncated PCA (irlba).
Hover for detailed sample information.
Top-10 most expressed genes across samples - AGDS_DS384_Huh7_TGFb_SB_MOA_02? The pie chart shows the top 10 most highly expressed genes, with each slice representing their percentage of total gene expression.
Hover for detailed sample information.
Top-10 most expressed biotypes across samples - AGDS_DS384_Huh7_TGFb_SB_MOA_02? The pie chart shows the top 10 most highly expressed gene biotypes, with each slice representing their percentage of total gene expression.
Hover for detailed sample information.
UMI statistics
Advanced QC: UMI duplication statistics
Library? FASTQ name of the BRB-seq library
Nb UMI counts? Number of the UMI counts (i.e. demultiplexed & mapped to the exons)
% UMI counts? Overall % of the reads comming from unique molecules
AGDS_DS384_Huh7_TGFb_SB_MOA_01
145132181
54.22
AGDS_DS384_Huh7_TGFb_SB_MOA_02
125053686
57.15
rRNA statistics
Advanced QC: rRNA mapping statistics
Library? FASTQ name of the BRB-seq library
Nb of rRNA? Number of reads mapped to rRNA using bbmap tool
% of rRNA? Overall % of the reads comming from rRNA
