Rui:LabNotes/SingleCell/2014-7-3

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Primary analysis on 20 chips of hNuc BA8[edit]

  • Outline ~1000 sets for hNuc BA8
  • Singles filtering criteria
  • DES -> biomarker

File:Brain-BAs.jpg

Sample list[edit]

  • Sample ID: YYYYMMDD-#Cxx, e.g. 20131219-0C25
  • Ensure sample IDs consistent across all files

File:20chips Samplelist.png

Basic mapping statistics[edit]

  • Each panel is ordered by chips (from 1st to 20th chip).
  • Each chip is ordered by 0hNuc, 1hNuc and mhNuc.
  • Some extremes: chip 13 vs chip 15

File:20chips total-reads.png

File:20chips mapRate.png

File:20chips mapRate-relative.png

File:20chips genomicRegion.png

File:20chips detected.png

ERCC basics[edit]

  • ERCC needs to be uniform across different chips, otherwise it can't used to normalize singles data.
  • TPM calling of ERCC has some inconsistency for a few samples
  • R is unrelated with number of ERCC called

File:ERCC TPM.png

File:ERCC fpkm.png

File:ERCC r.png

Re-organizing samples for quality filtering[edit]

Separation based on different criteria[edit]

  • To see which criteria can separate 0hNuc and 1hNuc well
  • To set up quality filter

File:Pcr hg19.jpg File:Pcr hg19 relative.jpg

File:GenomicRegions.jpg File:DetectedGenes.jpg

Sample shuffle based on different criteria[edit]

  • Based on hg19 absolute percentage

File:Pcr hg19 base.jpg

File:Pcr hg19 relative-pcr hg19.jpg

File:GeneDetect-pcr hg19.jpg

  • Based on hg19 relative percentage

File:Pcr hg19 relative base.jpg

File:Pcr hg19-pcr hg19 relative.jpg

File:GeneDetect-pcr hg19 relative.jpg

Reads vs genes/ERCC[edit]

  • Total reads vs mapped reads

File:Tread-hg19.jpg File:Tread-ERCC.jpg

  • Total/hg19 reads vs detected genes

File:Tread-genes.jpg File:Hg19-gene.jpg