Rui:LabNotes/SingleCell/2014-7-3

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Primary analysis on 20 chips of hNuc BA8

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

Sample list

File:20chips Samplelist.png

Basic mapping statistics

  • Each panel is ordered by chips (from 1st to 20th chip).
  • Each chip is ordered by 0hNuc, 1hNuc and mhNuc.

File:20chips total-reads.png

File:20chips mapRate.png

File:20chips mapRate-relative.png

File:20chips genomicRegion.png

File:20chips detected.png

ERCC basics

  • 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

  • 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