Last updated: 2020-04-10
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Knit directory: Comparative_APA/analysis/
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Rmd | 4a1eaf2 | brimittleman | 2020-01-09 | fix metadata out |
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Rmd | 93ced1e | brimittleman | 2020-01-09 | peak 2 pas |
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 1.6.0
Run ?workflowr for help getting started
In this analysis I want to make correct strand and coordinate bed files for the PAS .
The final PAS are in /project2/gilad/briana/Comparative_APA/data/Peaks_5perc/Peaks_5perc_either_HumanCoordHummanUsage.bed
I will fix the strand and put them in a PAS folder
mkdir ../data/PAS
#fix strand
PAS=read.table("../data/Peaks_5perc/Peaks_5perc_either_HumanCoordHummanUsage.bed", header=T,stringsAsFactors = F) %>% mutate(strandFix=ifelse(strand =="+","-","+")) %>% dplyr::select(-strand)
write.table(PAS,"../data/PAS/PAS_5perc_either_HumanCoordHummanUsage.bed",col.names = F, row.names = F, quote = F, sep="\t")
sort -k1,1 -k2,2n ../data/PAS/PAS_5perc_either_HumanCoordHummanUsage.bed > ../data/PAS/PAS_5perc_either_HumanCoordHummanUsage.sort.bed
strandinfo=PAS %>% dplyr::select(PAS, strandFix)
PASChimpUsage=read.table("../data/Peaks_5perc/Peaks_5perc_either_bothUsage.txt",header=T,stringsAsFactors = F) %>% inner_join(strandinfo, by="PAS") %>% dplyr::select(chr,start,end, PAS,Chimp, strandFix)
write.table(PASChimpUsage,"../data/PAS/PAS_5perc_either_HumanCoordChimpUsage.bed",col.names = F, row.names = F, quote = F, sep="\t")
Lift to get the chimp coordinates:
sbatch Lift5perPAS.sh
sort -k1,1 -k2,2n ../data/PAS/PAS_5perc_either_ChimpCoordChimpUsage.bed > ../data/PAS/PAS_5perc_either_ChimpCoordChimpUsage.sort.bed
Metadata=read.table("../data/Peaks_5perc/Peaks_5perc_either_bothUsage.txt",header=T,stringsAsFactors = F) %>% inner_join(strandinfo, by="PAS")
write.table(Metadata,"../data/PAS/PAS_5perc_either_HumanCoord_BothUsage_meta.txt",col.names = T, row.names = F, quote = F, sep="\t")
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_1.6.0 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_1.0.2 cellranger_1.1.0 plyr_1.8.4 compiler_3.5.1
[5] pillar_1.3.1 later_0.7.5 git2r_0.26.1 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] promises_1.0.1 htmltools_0.3.6 rvest_0.3.2 assertthat_0.2.0
[45] colorspace_1.3-2 httpuv_1.4.5 stringi_1.2.4 lazyeval_0.2.1
[49] munsell_0.5.0 broom_0.5.1 crayon_1.3.4