Introduction

We are interested in ATAC coverage around the TET2 gene: chr4:105013948-105412731

Here are the number of reads for the celltype split BAMs.

./FLW3/outs/atac_possorted_b_cells.bam 55042641 ./FLW3/outs/atac_possorted_dendritic_cells.bam 31361602 ./FLW3/outs/atac_possorted_monocytes.bam 77831616 ./FLW3/outs/atac_possorted_nk_cells.bam 46527668 ./FLW3/outs/atac_possorted_t_cells.bam 247420471

./FLW5/outs/atac_possorted_b_cells.bam 21031930 ./FLW5/outs/atac_possorted_dendritic_cells.bam 52944321 ./FLW5/outs/atac_possorted_monocytes.bam 90573275 ./FLW5/outs/atac_possorted_nk_cells.bam 47252636 ./FLW5/outs/atac_possorted_t_cells.bam 57226673

par(mfrow=c(6,1))
mar = c(3.1, 2.1, 2.1, 1.1)
# B CELLS
SCALE=76074571
x <- read.table("b_cells.bam.profile")
x <- subset(x,V1=="chr4")
x <- subset(x,V2>=105013948 & V2<=105412731)
plot(x$V2,x$V3/SCALE*1000000,type="l",bty="n",ylim=c(0,3.5), ylab="depth",xaxt = "n",xlab="",)
mtext("B cells") #3.4177

# DENDRITIC CELLS
SCALE=84305923
x <- read.table("dendritic_cells.bam.profile")
x <- subset(x,V1=="chr4")
x <- subset(x,V2>=105013948 & V2<=105412731)
plot(x$V2,x$V3/SCALE*1000000,type="l",bty="n",ylim=c(0,3.5), ylab="depth",xaxt = "n",xlab="")
mtext("Dendritic cells")

# MONOCYTES
SCALE=168404891
x <- read.table("monocytes.bam.profile")
x <- subset(x,V1=="chr4")
x <- subset(x,V2>=105013948 & V2<=105412731)
plot(x$V2,x$V3/SCALE*1000000,type="l",bty="n",ylim=c(0,3.5), ylab="depth",xaxt = "n",xlab="")
mtext("Monocytes") #3.390638

# NK CELLS
SCALE=93780304
x <- read.table("nk_cells.bam.profile")
x <- subset(x,V1=="chr4")
x <- subset(x,V2>=105013948 & V2<=105412731)
plot(x$V2,x$V3/SCALE*1000000,type="l",bty="n",ylim=c(0,3.5), ylab="depth",xaxt = "n",xlab="")
mtext("NK cells")

# T CELLS
SCALE=304647144
x <- read.table("t_cells.bam.profile")
x <- subset(x,V1=="chr4")
x <- subset(x,V2>=105013948 & V2<=105412731)
plot(x$V2,x$V3/SCALE*1000000,type="l",bty="n",ylim=c(0,3.5), ylab="depth",xaxt = "n",xlab="")
mtext("T cells")

# gene feature
#chr4:105146876-105279803
plot(x$V2,x$V3,type="p",cex=0,bty="n",ylim=c(0,2),xlab="chr4" , yaxt = "n", ylab="")
text(105213340,1.5,"TET2",cex=2)
arrows(x0=105146876,x1=105279803,y0=1,y1=1)

Session information

For reproducibilty.

sessionInfo()
## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.35     R6_2.5.1          fastmap_1.1.1     xfun_0.43        
##  [5] cachem_1.0.8      knitr_1.46        htmltools_0.5.8.1 rmarkdown_2.26   
##  [9] lifecycle_1.0.4   cli_3.6.2         sass_0.4.9        jquerylib_0.1.4  
## [13] compiler_4.4.0    highr_0.10        tools_4.4.0       evaluate_0.23    
## [17] bslib_0.7.0       yaml_2.3.8        rlang_1.1.3       jsonlite_1.8.8