bd logoRhapsody Sequence Analysis Pipeline SampleMultiplexDemo
Pipeline Version: 2.0rc1
Sat May 27 2023 16:47:16 GMT+0000 (Coordinated Universal Time)

Summary

Library
Total Reads in FASTQ
Pct Reads Passing Quality Filter
Pct CellLabel UMI Aligned Uniquely
SampleMultiplexDemo 57,920,558 97.07% 95.85%
Putative Cells

5,674

Bioproduct Type
Aligned Reads By Type
Mean Reads per Cell
Mean Molecules per Cell
mRNA 38,030,956 4,479.16 536.06
Sample Tags 14,434,842 1,168.98 -

Graphs

Sequence Quality

Library
Total Reads in FASTQ
Pct Read Pair Overlap
Pct Reads Too Short
Pct Reads Low Base Quality
Pct Reads High SNF
Pct Reads Filtered Out
Total Reads After Quality Filtering
SampleMultiplexDemo 57,920,558 0.09% 0.11% 1.79% 1.03% 2.93% 56,223,468

Library Quality

Library
Total Filtered Reads
Pct Q30 Bases in Filtered R2
Pct CellLabel UMI
Pct CellLabel UMI Aligned Uniquely
Pct Reads Useful
SampleMultiplexDemo 56,223,468 77.86% 96.68% 95.85% 93.32%

Alignment Categories

Library
CellLabel UMI Reads
Annotated Transcriptome Pct
Introns Pct
Intergenic Regions Pct
Antisense Pct
Not Unique Pct
Ambiguous Pct
No Feature Pct
AbSeq Pct
Sample Tag Pct
VDJ TCR Pct
VDJ BCR Pct
Unaligned Pct
SampleMultiplexDemo 54,356,832 72.25% 0% 0% 0.14% 0.06% 0% 0% 0% 26.69% 0% 0% 0.86%

Reads and Molecules

Bioproduct Type
Aligned Reads By Type
Total Raw Molecules
Total RSEC Molecules
Mean Raw Sequencing Depth
Mean RSEC Sequencing Depth
Sequencing Saturation
mRNA 38,030,956 9,231,528 8,098,503 4.12 4.7 92.04

Cells

Putative Cells


Basic Algorithm Cells
Bioproduct Type
Pct Reads from Putative Cells
Mean Reads per Cell
Median Reads per Cell
Mean Molecules per Cell
Median Molecules per Cell
Mean Bioproducts per Cell
Median Bioproducts per Cell
Total Bioproducts Detected
mRNA 66.83% 4,479.16 2,699 536.06 337 80.35 76 376

Sample Multiplexing

Valid Reads aligned to Sample Tags

Pct Reads from Putative Cells

Sample Tag
Sample Names
Raw Reads
Pct of Raw Reads
Cells Called
Pct of Putative Cells Called
Raw Reads in Called Cells
Mean Reads per Called Cell
All_Tags - 14,434,842 100% 5,674 100% 6,632,771 1,168.98
SampleTag01_hs PBMCDonor1 3,988,514 27.63% 2,225 39.21% 1,530,761 687.98
SampleTag02_hs PBMCDonor2 10,443,250 72.35% 3,227 56.87% 5,102,010 1,581.04
SampleTag03_hs - 116 0% 0 0% 0 0
SampleTag04_hs - 80 0% 0 0% 0 0
SampleTag05_hs - 702 0% 0 0% 0 0
SampleTag06_hs - 1,939 0.01% 0 0% 0 0
SampleTag07_hs - 100 0% 0 0% 0 0
SampleTag08_hs - 48 0% 0 0% 0 0
SampleTag09_hs - 11 0% 0 0% 0 0
SampleTag10_hs - 3 0% 0 0% 0 0
SampleTag11_hs - 10 0% 0 0% 0 0
SampleTag12_hs - 69 0% 0 0% 0 0
Multiplet - - - 187 3.3% - -
Undetermined - - - 35 0.62% - -

Pipeline Inputs

Pipeline version: 2.0rc1

Pipeline Start Time: Sat May 27 2023 16:47:16 GMT+0000 (Coordinated Universal Time)

AbSeq Reference:
  • No value
Reference Files Archive:
  • No value
Supplemental Reference:
  • No value
Targeted Reference:
  • BD_Rhapsody_Immune_Response_Panel_Hs.fasta
Reads:
  • SampleMultiplexDemo_S1_L001_R1_001.fastq.gz
  • SampleMultiplexDemo_S1_L001_R2_001.fastq.gz
Multiplexing Settings

Sample Tags Version: hs
Tag Names: 1-PBMCDonor1, 2-PBMCDonor2

VDJ Settings

VDJ Species Version: No value

Putative Cell Calling Settings

Enable Refined Putative Cell Calling: False
Exact Cell Count: No value
Expected Cell Count: No value
Putative Cell Call: mRNA

Exclude Intronic reads: False

Generate Bam output: False

Metric Alerts

(Under development)
  For the [Sample_Tags] bioproduct type, the [ST_Pct_Reads_from_Putative_Cells] metric value of 49.13% is less than 60% (Sample Multiplexing section, Targeted assay threshold).
   
  • May be due to low cell viability or inefficient cell washing.
  • Confirm using scanner metrics that an appropriate proportion of live cells were loaded, or contact customer support for suggestions on cell washing.
.fdsafsdfsdf