QC filtered sequencing reads
Evangelyn Sim
2/2/2021
Last updated: 2021-02-19
Checks: 6 1
Knit directory: Human_Development_RNAseq_bulk/
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Introduction
In the GEO submission 3 processed files were uploaded.
- hrna_dev_mf_fulllen_se_strrev_q30.mx.all.fix_filt.csv
- hrna_dev_mf_fulllen_se_strrev_q30.mx.all.MvsF.fix_filt.csv
- hrna_dev_mf_fulllen_se_strrev_q30.mx.all_unfiltered.csv
They have been uploaded in the /output folder and will be used below to generate different figures.
Used libraries and functions
library(edgeR)Loading required package: limmalibrary(limma)
library(Glimma)
library(gplots)
Attaching package: 'gplots'The following object is masked from 'package:stats':
lowessCount per million reads
rm1 <- read.csv("/group/card2/Evangelyn_Sim/Transcriptome_chromatin_human/Sequencing_ATAC_RNA/GITHUB/Human_Development_RNAseq_bulk/output/hrna_dev_mf_fulllen_se_strrev_q30.mx.all.fix_filt.csv", row.names = 1)
info = read.delim("/group/card2/Evangelyn_Sim/Transcriptome_chromatin_human/Sequencing_ATAC_RNA/GITHUB/Human_Development_RNAseq_bulk/output/RNAseq_samplesheet.txt", header = TRUE, sep = "\t")
m = match(info$ID,names(rm1))
rm2 = rm1[,m]
rm1 = rm2
mycpm = cpm(rm1)
summary(mycpm) Fetal1 Fetal2 Fetal3 Fetal4
Min. : 0.000 Min. : 0.00 Min. : 0.00 Min. : 0.00
1st Qu.: 1.605 1st Qu.: 1.47 1st Qu.: 1.65 1st Qu.: 1.14
Median : 8.431 Median : 7.94 Median : 8.73 Median : 6.62
Mean : 54.448 Mean : 54.45 Mean : 54.45 Mean : 54.45
3rd Qu.: 36.557 3rd Qu.: 35.36 3rd Qu.: 35.99 3rd Qu.: 31.24
Max. :26895.478 Max. :35265.37 Max. :31887.65 Max. :40646.07
Fetal5 Fetal6 Young1 Young2
Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00
1st Qu.: 1.03 1st Qu.: 1.22 1st Qu.: 0.97 1st Qu.: 0.81
Median : 5.88 Median : 6.92 Median : 6.90 Median : 5.27
Mean : 54.45 Mean : 54.45 Mean : 54.45 Mean : 54.45
3rd Qu.: 29.09 3rd Qu.: 31.21 3rd Qu.: 32.44 3rd Qu.: 27.88
Max. :33640.91 Max. :44477.77 Max. :50920.65 Max. :54059.52
Young3 Young4 Adult1 Adult2
Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00
1st Qu.: 1.03 1st Qu.: 0.72 1st Qu.: 0.69 1st Qu.: 0.54
Median : 6.41 Median : 5.51 Median : 4.20 Median : 4.01
Mean : 54.45 Mean : 54.45 Mean : 54.45 Mean : 54.45
3rd Qu.: 29.10 3rd Qu.: 28.79 3rd Qu.: 20.31 3rd Qu.: 24.44
Max. :53094.50 Max. :52056.09 Max. :304053.04 Max. :76411.57
Adult3 Adult4 Adult5 Adult6
Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00
1st Qu.: 0.88 1st Qu.: 0.47 1st Qu.: 0.73 1st Qu.: 0.79
Median : 5.12 Median : 3.31 Median : 4.47 Median : 4.90
Mean : 54.45 Mean : 54.45 Mean : 54.45 Mean : 54.45
3rd Qu.: 23.54 3rd Qu.: 18.72 3rd Qu.: 22.94 3rd Qu.: 25.23
Max. :76477.86 Max. :278442.84 Max. :68068.79 Max. :52599.18
Adult7 Adult8 Adult9 Adult10
Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00
1st Qu.: 0.58 1st Qu.: 0.70 1st Qu.: 0.67 1st Qu.: 0.51
Median : 3.72 Median : 4.82 Median : 4.27 Median : 3.77
Mean : 54.45 Mean : 54.45 Mean : 54.45 Mean : 54.45
3rd Qu.: 22.44 3rd Qu.: 26.55 3rd Qu.: 22.95 3rd Qu.: 23.82
Max. :63496.93 Max. :61823.40 Max. :78336.05 Max. :74051.19
Adult11
Min. : 0.00
1st Qu.: 0.70
Median : 4.33
Mean : 54.45
3rd Qu.: 23.07
Max. :58908.31 x <- DGEList(rm1)
names(x)[1] "counts" "samples"logcountsx = cpm(x, log = T)
write.csv(logcountsx, file = "/group/card2/Evangelyn_Sim/Transcriptome_chromatin_human/Sequencing_ATAC_RNA/GITHUB/Human_Development_RNAseq_bulk/output/logCPM_hrna_dev_mf_fulllen_se_strrev_q30.mx.all.fix_filt.csv")
barplot(x$samples$lib.size, names=colnames(x), las=2, col = c("violetred4","darkgoldenrod2","tomato")[info$Group], main = "Library size")
boxplot(logcountsx, xlab="", ylab="Log2 counts per million", las=2, col = c("violetred4","darkgoldenrod2","tomato")[info$Group])
abline(h=median(logcountsx), col="navy")
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /hpc/software/installed/R/3.6.1/lib64/R/lib/libRblas.so
LAPACK: /hpc/software/installed/R/3.6.1/lib64/R/lib/libRlapack.so
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
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gplots_3.1.0 Glimma_1.12.0 edgeR_3.26.8 limma_3.40.6
[5] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 pillar_1.4.6 compiler_3.6.1 later_1.1.0.1
[5] git2r_0.27.1 highr_0.8 bitops_1.0-6 tools_3.6.1
[9] digest_0.6.27 jsonlite_1.7.0 evaluate_0.14 lifecycle_0.2.0
[13] tibble_3.0.3 lattice_0.20-41 pkgconfig_2.0.3 rlang_0.4.7
[17] rstudioapi_0.11 yaml_2.2.1 xfun_0.18 stringr_1.4.0
[21] knitr_1.30 caTools_1.18.0 gtools_3.8.2 fs_1.5.0
[25] vctrs_0.3.2 locfit_1.5-9.4 rprojroot_1.3-2 grid_3.6.1
[29] glue_1.4.2 R6_2.5.0 rmarkdown_2.5 magrittr_1.5
[33] whisker_0.4 backports_1.1.10 promises_1.1.1 ellipsis_0.3.1
[37] htmltools_0.5.0 httpuv_1.5.4 KernSmooth_2.23-17 stringi_1.5.3
[41] crayon_1.3.4