bd logoRhapsody Sequence Analysis Pipeline HumanImmResDemo
Pipeline Version: 2.0rc1
Sat May 27 2023 16:56:07 GMT+0000 (Coordinated Universal Time)

Summary

Library
Total Reads in FASTQ
Pct Reads Passing Quality Filter
Pct CellLabel UMI Aligned Uniquely
HumanImmResDemo 22,167,998 90.7% 93.97%
Putative Cells

3,221

Bioproduct Type
Aligned Reads By Type
Mean Reads per Cell
Mean Molecules per Cell
mRNA 18,509,408 4,083.22 640.3

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
HumanImmResDemo 22,167,998 0.09% 0.08% 4.3% 4.92% 9.3% 20,106,655

Library Quality

Library
Total Filtered Reads
Pct Q30 Bases in Filtered R2
Pct CellLabel UMI
Pct CellLabel UMI Aligned Uniquely
Pct Reads Useful
HumanImmResDemo 20,106,655 84.89% 94.61% 93.97% 92.06%

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
HumanImmResDemo 19,022,066 99.14% 0% 0% 0.17% 0.02% 0% 0% 0% 0% 0% 0% 0.68%

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 18,509,408 5,730,351 5,303,421 3.23 3.49 84.21

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 71.06% 4,083.22 2,754 640.3 430 103.64 98 368

Pipeline Inputs

Pipeline version: 2.0rc1

Pipeline Start Time: Sat May 27 2023 16:56:07 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:
  • HumanImmResDemo_S1_L001_R1_001.fastq.gz
  • HumanImmResDemo_S1_L001_R2_001.fastq.gz
Multiplexing Settings

Sample Tags Version: No value
Tag Names:

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 [HumanImmResDemo] library, the [Pct_Reads_Low_Base_Quality] metric value of 4.3% is greater than 2% (Sequencing Quality section, Targeted assay threshold).
   
  • May be due to issues during sequencing. Check for appropriate cluster density on sequencer.
  • If running a low complexity library, consider adjusting PhiX input.
  • This may also result from long read lengths, in which case reads should be trimmed before running the BD sequencing analysis pipeline.
  For the [HumanImmResDemo] library, the [Pct_Reads_High_SNF] metric value of 4.92% is greater than 4% (Sequencing Quality section, Targeted assay threshold).
   
  • Check for the presence of small products in QC traces. This can also be expected from long read libraries.
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