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
Sample list[edit]
- Sample ID: YYYYMMDD-#Cxx, e.g. 20131219-0C25
- Ensure sample IDs consistent across all files
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 mapRate-relative.png
File:20chips genomicRegion.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
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 relative-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