Last updated: 2019-09-26
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Knit directory: apaQTL/analysis/
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File | Version | Author | Date | Message |
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Rmd | aa30fa2 | brimittleman | 2019-09-26 | add new dt plots analysis |
I want to make new deeptools plots for figure 1a with 5 individuals in each.
I need to merge bam files then convert to BW.
mkdir ../data/FiveMergedBam/
sbatch merge5RNAbam.sh
sbatch merge53prime.sh
Next I need to make bigwigs for each of these:
mkdir ../data/FiveMergedBW
sbatch bam2bw.sh ../data/FiveMergedBam/RNAeuvadisBams_5mergeds.sort.bam ../data/FiveMergedBW/RNAeuvadisBams_5mergeds.sort.bw
sbatch bam2bw.sh ../data/FiveMergedBam/threeprimeN_Bams_5mergeds.sort.bam ../data/FiveMergedBam/threeprimeN_Bams_5mergeds.sort.bw
sbatch NuclearandRNA5samp_dtplots.sh
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.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
loaded via a namespace (and not attached):
[1] workflowr_1.4.0 Rcpp_1.0.2 digest_0.6.18 rprojroot_1.3-2
[5] backports_1.1.2 git2r_0.25.2 magrittr_1.5 evaluate_0.12
[9] stringi_1.2.4 fs_1.3.1 whisker_0.3-2 rmarkdown_1.10
[13] tools_3.5.1 stringr_1.3.1 glue_1.3.0 yaml_2.2.0
[17] compiler_3.5.1 htmltools_0.3.6 knitr_1.20