2  Cell Ranger

2.1 Cell Ranger metrics

suppressPackageStartupMessages({
    library(tidyverse)
    library(kableExtra)
    })

dataset.loc <- "~/Dropbox/SyncBriefcase/LAB/UK/scRNA_Akhil/cellRanger_data"
metrics_files <- list.files(path = dataset.loc, pattern = "metrics_summary",
                      full.names = T, recursive = T)
metrics <- map(metrics_files,
               read.csv) |> 
    list_rbind() |> 
    t() |> 
    as.data.frame() |> 
    set_names(str_split_i(metrics_files,"/",10))

kbl(metrics) |> 
  kable_styling("striped")

	464	465	492	496	497	502	504	505
Estimated.Number.of.Cells	14,733	10,564	11,878	9,581	13,145	12,743	11,343	11,960
Mean.Reads.per.Cell	31,645	49,477	43,541	55,427	43,953	37,088	42,368	45,920
Median.Genes.per.Cell	3,274	3,727	3,638	3,709	3,544	3,425	3,350	3,700
Number.of.Reads	466,228,773	522,674,656	517,177,074	531,049,253	577,755,963	472,607,562	480,577,300	549,202,130
Valid.Barcodes	92.9%	92.8%	93.5%	93.5%	93.4%	93.8%	93.2%	93.9%
Valid.UMIs	98.9%	99.0%	98.9%	98.9%	99.0%	98.9%	98.9%	99.0%
Sequencing.Saturation	56.4%	64.0%	61.4%	66.3%	63.7%	59.8%	64.2%	63.1%
Q30.Bases.in.Barcode	97.6%	97.5%	97.8%	97.6%	97.7%	97.6%	97.8%	97.7%
Q30.Bases.in.RNA.Read	96.5%	96.6%	96.6%	96.8%	96.7%	96.9%	96.7%	96.7%
Q30.Bases.in.UMI	98.2%	98.2%	98.3%	98.2%	98.2%	98.2%	98.4%	98.3%
Reads.Mapped.to.Genome	95.8%	95.9%	96.5%	96.7%	96.7%	96.6%	96.5%	96.6%
Reads.Mapped.Confidently.to.Genome	94.0%	93.8%	94.5%	94.8%	94.8%	94.7%	94.4%	94.9%
Reads.Mapped.Confidently.to.Intergenic.Regions	10.1%	10.8%	9.0%	9.1%	8.6%	8.9%	9.9%	8.4%
Reads.Mapped.Confidently.to.Intronic.Regions	23.4%	23.5%	21.2%	19.7%	21.2%	18.7%	19.2%	21.9%
Reads.Mapped.Confidently.to.Exonic.Regions	60.4%	59.5%	64.3%	65.9%	65.0%	67.2%	65.3%	64.6%
Reads.Mapped.Confidently.to.Transcriptome	79.4%	78.8%	81.4%	81.4%	81.8%	82.0%	80.3%	82.4%
Reads.Mapped.Antisense.to.Gene	4.2%	3.9%	3.9%	4.0%	4.1%	3.6%	3.9%	3.8%
Fraction.Reads.in.Cells	92.1%	91.7%	93.0%	90.2%	91.7%	91.3%	91.5%	92.2%
Total.Genes.Detected	26,264	25,420	25,737	26,036	25,760	25,613	25,386	25,842
Median.UMI.Counts.per.Cell	8,897	11,378	11,134	11,521	10,629	9,845	9,659	11,318