Last updated: 2019-07-17
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Knit directory: apaQTL/analysis/
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Rmd | 2572d13 | brimittleman | 2019-07-16 | add compare annotated and additional coverage |
I want to make some additional plots of the coverage of 3’ seq at locations. I will use the deeptools plots.
For these I will make seperate total and nuclear plots
library(tidyverse)
── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1 ✔ purrr 0.3.2
✔ tibble 2.1.1 ✔ dplyr 0.8.0.1
✔ tidyr 0.8.3 ✔ stringr 1.3.1
✔ readr 1.3.1 ✔ forcats 0.3.0
── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
library(workflowr)
This is workflowr version 1.4.0
Run ?workflowr for help getting started
I will use the PAS called using LCL pacbio data. Ankeeta created the file.
mkdir ../data/pacbio
cp /project2/yangili1/ankeetashah/APA_tools/pacbio_3/PACBIO.ANNOTATED.USAGE.BED ../data/pacbio/PACBIO.Annotated.usage.PublicData.bed
#remove chr and sort
sed 's/^chr//' ../data/pacbio/PACBIO.Annotated.usage.PublicData.bed | sort -k1,1 -k2,2n > ../data/pacbio/pacbioPACBIO.Annotated.usage.PublicData.sort.bed
../data/pacbio/pacbioPACBIO.Annotated.usage.PublicData.sort.bed
sbatch pacbioDT.sh
Subset to those falling in intronic regions. I can do this by intersecting with my original annotation file.
/project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefSeq_FormatedallAnnotation.sort.bed
sbatch annotatePacBioPASregion.sh
I need to parse this like I did my original file.
pacbio=read.table("../data/pacbio/pacbioPACBIO.Annotated.usage.PublicData.sort_withAnnotationparsed.SAF", header = T,stringsAsFactors = F) %>% separate(GeneID, into =c("PASnum", "chr", "start","end", "strand","geneID"),sep=":") %>% separate(geneID, into = c("gene", "loc"), sep="_") %>% filter(loc=="intron") %>% mutate(pASid=paste(PASnum, gene, sep=":"), score=".") %>% select(Chr, Start, End, pASid, score, strand)
write.table(pacbio, file="../data/pacbio/IntronicPacBioPAS.bed", col.names = F, row.names = F, quote = F, sep="\t")
sbatch pacbioIntronicDT.sh
sbatch IntronicPASDT.sh
python chooseAnno2PAS_pacbio.py ../data/pacbio/pacbioPACBIO.Annotated.usage.PublicData.sort_withAnnotation.bed ../data/pacbio/pacbioPACBIO.Annotated.usage.PublicData.sort_withAnnotationparsed.SAF
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
other attached packages:
[1] workflowr_1.4.0 forcats_0.3.0 stringr_1.3.1 dplyr_0.8.0.1
[5] purrr_0.3.2 readr_1.3.1 tidyr_0.8.3 tibble_2.1.1
[9] ggplot2_3.1.1 tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 cellranger_1.1.0 plyr_1.8.4 compiler_3.5.1
[5] pillar_1.3.1 git2r_0.25.2 highr_0.7 tools_3.5.1
[9] digest_0.6.18 lubridate_1.7.4 jsonlite_1.6 evaluate_0.12
[13] nlme_3.1-137 gtable_0.2.0 lattice_0.20-38 pkgconfig_2.0.2
[17] rlang_0.4.0 cli_1.1.0 rstudioapi_0.10 yaml_2.2.0
[21] haven_1.1.2 withr_2.1.2 xml2_1.2.0 httr_1.3.1
[25] knitr_1.20 hms_0.4.2 generics_0.0.2 fs_1.3.1
[29] rprojroot_1.3-2 grid_3.5.1 tidyselect_0.2.5 glue_1.3.0
[33] R6_2.3.0 readxl_1.1.0 rmarkdown_1.10 modelr_0.1.2
[37] magrittr_1.5 whisker_0.3-2 backports_1.1.2 scales_1.0.0
[41] htmltools_0.3.6 rvest_0.3.2 assertthat_0.2.0 colorspace_1.3-2
[45] stringi_1.2.4 lazyeval_0.2.1 munsell_0.5.0 broom_0.5.1
[49] crayon_1.3.4