Rui:LabNotes/SingleCell/2014-7-3: Difference between revisions
Jump to navigation
Jump to search
>RuiLiu |
>RuiLiu m (→ERCC basics) |
||
(11 intermediate revisions by the same user not shown) | |||
Line 3: | Line 3: | ||
* Singles filtering criteria | * Singles filtering criteria | ||
* DES -> biomarker | * DES -> biomarker | ||
[[Image:Brain-BAs.jpg|800px]] | |||
===Sample list=== | ===Sample list=== | ||
* Sample ID: YYYYMMDD-#Cxx, e.g. 20131219-0C25 | |||
* Ensure sample IDs consistent across all files | |||
[[Image:20chips_Samplelist.png|800px]] | [[Image:20chips_Samplelist.png|800px]] | ||
Line 10: | Line 14: | ||
* Each panel is ordered by chips (from 1st to 20th chip). | * Each panel is ordered by chips (from 1st to 20th chip). | ||
* Each chip is ordered by 0hNuc, 1hNuc and mhNuc. | * Each chip is ordered by 0hNuc, 1hNuc and mhNuc. | ||
* Some extremes: chip 13 vs chip 15 | |||
[[Image:20chips_total-reads.png|800px]] | [[Image:20chips_total-reads.png|800px]] | ||
Line 22: | Line 27: | ||
===ERCC basics=== | ===ERCC basics=== | ||
* 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 | * TPM calling of ERCC has some inconsistency for a few samples | ||
* R is unrelated with number of ERCC called | * R is unrelated with number of ERCC called | ||
Line 31: | Line 37: | ||
[[Image:ERCC_r.png|800px]] | [[Image:ERCC_r.png|800px]] | ||
===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 | |||
[[Image:pcr_hg19.jpg|400px]] [[Image:pcr_hg19_relative.jpg|400px]] | |||
[[Image:genomicRegions.jpg|400px]] [[Image:detectedGenes.jpg|400px]] | |||
====Sample shuffle based on different criteria==== | |||
* Based on hg19 absolute percentage | |||
[[Image:pcr_hg19_base.jpg|800px]] | |||
[[Image:pcr_hg19_relative-pcr_hg19.jpg|800px]] | |||
[[Image:geneDetect-pcr_hg19.jpg|800px]] | |||
* Based on hg19 relative percentage | |||
[[Image:pcr_hg19_relative_base.jpg|800px]] | |||
[[Image:pcr_hg19-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]] |
Latest revision as of 17:47, 7 July 2014
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