Rui:LabNotes/SingleCell/2014-7-3: Difference between revisions
Jump to navigation
Jump to search
>RuiLiu |
>RuiLiu |
||
Line 51: | Line 51: | ||
[[Image:geneDetect-pcr_hg19_relative.jpg|800px]] | [[Image:geneDetect-pcr_hg19_relative.jpg|800px]] | ||
==Reads vs genes/ERCC== | |||
* Total reads vs mapped reads | |||
[[Image:Tread-hg19.jpg|400px]] [[Image:Tread-ERCC.jpg|400px]] | |||
* Total/hg19 reads vs detected genes | |||
[[Image:Tread-genes.jpg|400px]] [[Image:hg19-gene.jpg|400px]] |
Revision as of 04:37, 7 July 2014
Primary analysis on 20 chips of hNuc BA8
- Outline ~1000 sets for hNuc BA8
- Singles filtering criteria
- DES -> biomarker
Sample list
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 mapRate-relative.png
File:20chips genomicRegion.png
ERCC basics
- 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
Separation based on different criteria
- 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
- Based on hg19 absolute percentage
File:Pcr hg19 relative-pcr hg19.jpg
- Based on hg19 relative percentage
File:Pcr hg19-pcr hg19 relative.jpg
File:GeneDetect-pcr hg19 relative.jpg
Reads vs genes/ERCC
- Total reads vs mapped reads
File:Tread-hg19.jpg File:Tread-ERCC.jpg
- Total/hg19 reads vs detected genes