Pilot3: ensemble cell calling analysis
Christina Azodi
2022-03-02
Last updated: 2022-03-02
Checks: 5 2
Knit directory: BAUH_2020_MND-single-cell/analysis/
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Unstaged changes:
Modified: analysis/2022-01-07_pilot3_Cell-Calling-Comparison.Rmd
Modified: analysis/2022-02-28_pilot3_Cell-demultiplexing-Lenti.Rmd
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Modified: code/get_barcodes_to_use.R
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Ensemble approach
iPSC (Capture5) results
- Number of barcodes called as cell by 1+ methods: 55040
- Number of barcodes called as cell by 2+ methods: 47662
- Number of barcodes called as cell by 3+ methods: 38431
- Number of barcodes called as cell by 4+ methods: 18999
Very strong overlap between methods, current exception is that cellbender won’t return more cells than specified in the –total-droplets-included parameter. This parameter should be set to be a few thousand barcodes into the empty droplet plateau. Which I set to 20 for all captures, but should increase to at least 50k in a future run of cellbender.
c5 <- readRDS(paste0(ipsc_dir, "Capture5-GEX/combination_matrix.rds"))
UpSet(c5, set_order = c("CellRanger", "cellbender", "dropkick", "DropletQC"),
comb_col = c("#B0DBF1", "#253DA1", "#1D2570", "#000137")[comb_degree(c5)])
Capture 5
ACTION ITEM: rerun cellbender on iPSCs with –total-droplets-included=60k
MN captures
Capture 1
- Number of barcodes called as cell by 1+ methods: 12493
- Number of barcodes called as cell by 2+ methods: 8668
- Number of barcodes called as cell by 3+ methods: 5847
- Number of barcodes called as cell by 4+ methods: 3299
c1 <- readRDS(paste0(mn_dir, "Capture1-GEX/combination_matrix.rds"))
UpSet(c1, set_order = c("CellRanger", "cellbender", "dropkick", "DropletQC"),
comb_col = c("#B0DBF1", "#253DA1", "#1D2570", "#000137")[comb_degree(c1)])
Capture 1
Capture 2
- Number of barcodes called as cell by 1+ methods: 23732
- Number of barcodes called as cell by 2+ methods: 10782
- Number of barcodes called as cell by 3+ methods: 4810
- Number of barcodes called as cell by 4+ methods: 665
c2 <- readRDS(paste0(mn_dir, "Capture2-GEX/combination_matrix.rds"))
UpSet(c2, set_order = c("CellRanger", "cellbender", "dropkick", "DropletQC"),
comb_col = c("#B0DBF1", "#253DA1", "#1D2570", "#000137")[comb_degree(c2)])
Capture 2
Capture 3
- Number of barcodes called as cell by 1+ methods: 15890
- Number of barcodes called as cell by 2+ methods: 8334
- Number of barcodes called as cell by 3+ methods: 5761
- Number of barcodes called as cell by 4+ methods: 2497
c3 <- readRDS(paste0(mn_dir, "Capture3-GEX/combination_matrix.rds"))
UpSet(c3, set_order = c("CellRanger", "cellbender", "dropkick", "DropletQC"),
comb_col = c("#B0DBF1", "#253DA1", "#1D2570", "#000137")[comb_degree(c3)])
Capture 3
Capture 4
- Number of barcodes called as cell by 1+ methods: 27800
- Number of barcodes called as cell by 2+ methods: 20471
- Number of barcodes called as cell by 3+ methods: 10924
- Number of barcodes called as cell by 4+ methods: 644
c4 <- readRDS(paste0(mn_dir, "Capture4-GEX/combination_matrix.rds"))
UpSet(c4, set_order = c("CellRanger", "cellbender", "dropkick", "DropletQC"),
comb_col = c("#B0DBF1", "#253DA1", "#1D2570", "#000137")[comb_degree(c4)])
Capture 4
sessionInfo()R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.5 (Ootpa)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ComplexHeatmap_2.10.0 ggvenn_0.1.9 ggplot2_3.3.5
[4] data.table_1.14.2 tidyr_1.1.4 dplyr_1.0.7
[7] cowplot_1.1.1
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[25] xfun_0.28 pkgconfig_2.0.3 BiocGenerics_0.40.0
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[55] rjson_0.2.20 RColorBrewer_1.1-2 iterators_1.0.13
[58] tools_4.1.1 glue_1.6.0 purrr_0.3.4
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