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Perform single-cell RNA-seq analysis from FastQ files to cerebro file for 10XGenomics technology data.
Individual Analysis
- Alignment_countTable_GE,
- Alignment_countTable_ADT,
- Alignment_annotations_TCR_BCR,
- Droplets_QC_GE,
- Filtering_GE,
- Norm_DimRed_Eval_GE,
- Clust_Markers_Annot_GE,
- Adding_ADT,
- Adding_TCR,
- Adding_BCR,
- Cerebro.
Integrated Analysis *
Grouped Analysis *
- Integration analysis of several samples,
- Grouped analysis (no integration) of several samples,
- TCR for several samples together,
- BCR for several samples together,
- Improve cell annotation,
- ...
Resources of the Theory of single cell RNA-seq
v1.3
Pipeline details
Configuration
-
Parameter file
- Steps
- Alignment_countTable_GE
- Droplets_QC_GE
- Filtering_GE
- Norm_DimRed_Eval_GE
- Clust_Markers_Annot_GE
- Cerebro
- Alignment_countTable_ADT
- Adding_ADT
- Alignment_annotations_TCR_BCR
- Adding_TCR
- Adding_BCR
- Int_Norm_DimRed_Eval_GE
- Int_Clust_Markers_Annot_GE
- Int_Adding_ADT
- Int_Adding_TCR
- Int_Adding_BCR
- Grp_Norm_DimRed_Eval_GE
- Grp_Clust_Markers_Annot_GE
- Grp_Adding_ADT
- Grp_Adding_TCR
- Grp_Adding_BCR
- Additional files
Results help
- Arborescence of all results
-
Observations and weird results
- Not a threshold by emptyDrops
- Large and small cells into the same sample
- emptyDrops does't work well
- More than 15% mitochondrial RNA while I filtered them out at 15%
- Impact of empty droplets on umap
- Choose the right number of dimensions
- Be careful with the colors, they are sometimes misleading
- Impact of bias correction on umap
Complete Examples of school cases
Individual analysis :
1 sample (scRNA-seq + ADT + TCR + BCR)
Grouped/Integrated analysis :
2 samples (scRNA-seq + ADT + TCR + BCR)