Characterize orthologous peaks

Last updated: 2018-08-22

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File	Version	Author	Date	Message
Rmd	3a19b07	brimittleman	2018-08-22	add hg19 dist
html	d0d4599	brimittleman	2018-08-21	Build site.

I will use this analysis for QC on the orthologous peaks called in the liftover pipeline analysis.

Distance to ortho exon

I want to make sure the distances of the orthologous peaks to the nearest exon called in Bryans ortho exon files follow a similar distribution.

The orthologus exon files are in /project2/gilad/briana/genome_anotation_data/ortho_exon and the small version have just chr start end and exon name.

The ortho peak files are in /project2/gilad/briana/comparitive_threeprime/data/ortho_peaks/

I want the closest exon upstream, i will use bedtools closest:

distUpstreamexon.sh

#!/bin/bash

#SBATCH --job-name=disUpstreamexon
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=disUpstreamexon.out
#SBATCH --error=disUpstreamexon.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END


module load Anaconda3
source activate comp_threeprime_env

bedtools closest -id -D a -a /project2/gilad/briana/comparitive_threeprime/data/ortho_peaks/chimpOrthoPeaks.sort.bed  -b /project2/gilad/briana/genome_anotation_data/ortho_exon/2017_July_ortho_chimp.small.sort.bed > /project2/gilad/briana/comparitive_threeprime/data/dist_upexon/Chimp.distUpstreamexon.txt


bedtools closest -id -D a -a /project2/gilad/briana/comparitive_threeprime/data/ortho_peaks/humanOrthoPeaks.sort.bed -b /project2/gilad/briana/genome_anotation_data/ortho_exon/2017_July_ortho_human.small.sort.bed > /project2/gilad/briana/comparitive_threeprime/data/dist_upexon/Human.distUpstreamexon.txt

Import the files and plot the distances.

library(tidyverse)

── Attaching packages ──────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──

✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0

── Conflicts ─────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(workflowr)

This is workflowr version 1.1.1
Run ?workflowr for help getting started

library(cowplot)


Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

getwd()

[1] "/Users/bmittleman1/Documents/Gilad_lab/comparitive_threeprime/com_threeprime/analysis"

file.exists("../data/dist_upexon/Chimp.distUpstreamexon.txt")

[1] TRUE

chimp_dist=read.table("../data/dist_upexon/Chimp.distUpstreamexon.txt", col.names = c("peak_chr", "peak_start", "peak_end", "peak_name", "exon_chr", "exon_start", "exon_end", "exon_name", "dist"), stringsAsFactors = F) %>% mutate(logdis=log10(abs(dist) +1 ))

human_dist=read.table("../data/dist_upexon/Human.distUpstreamexon.txt", col.names = c("peak_chr", "peak_start", "peak_end", "peak_name", "exon_chr", "exon_start", "exon_end", "exon_name", "dist"),stringsAsFactors = F, skip=1) %>% mutate(logdis=log10(abs(dist) +1 ))

ch=ggplot(chimp_dist, aes(x=logdis)) + geom_density() + labs(x="log10 abs.value \n distance +1 ", title="Chimp distance to ortho exon")

hu=ggplot(human_dist, aes(x=logdis)) + geom_density()+ labs(x="log10 abs.value \n distance +1 ", title="Human distance to ortho exon")


plot_grid(ch, hu)

Expand here to see past versions of unnamed-chunk-4-1.png:

Version	Author	Date
d0d4599	brimittleman	2018-08-21

This is a good sanity check. The distributions are similar. I want to check this with the peaks from the human APAqtl study. I have the gencode exons and I will run bedtools cloests with this.

#!/bin/bash

#SBATCH --job-name=disUpstreamexon_hum
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=disUpstreamexon_hum.out
#SBATCH --error=disUpstreamexon_hum.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END


module load Anaconda3
source activate comp_threeprime_env

bedtools closest -id -D a -a /project2/gilad/briana/comparitive_threeprime/data/extra_anno/human_hg19_filteredPeaks.bed -b /project2/gilad/briana/comparitive_threeprime/data/extra_anno/gencode.hg19.v19.exons.bed > /project2/gilad/briana/comparitive_threeprime/data/dist_upexon/hg19.humanpeaks.distUpstreamexon.txt

update these files to remove the tab at the end.

hg19_dist=read.table("../data/dist_upexon/hg19.humanpeaks.distUpstreamexon.txt", col.names = c("peak_chr", "peak_start", "peak_end", "peak_cov","peak_strand", "peak_score", "exon_chr", "exon_start", "exon_end", "exon_name", "exon_score", "exon_strand", "dist"),stringsAsFactors = F, skip=1) %>% mutate(logdis=log10(abs(dist) +1 ))

ggplot(hg19_dist, aes(x=logdis)) + geom_density()+ labs(x="log10 abs.value \n distance +1 ", title="Hg19 peaks dist to upstream exon")

Session information

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] bindrcpp_0.2.2  cowplot_0.9.3   workflowr_1.1.1 forcats_0.3.0  
 [5] stringr_1.3.1   dplyr_0.7.6     purrr_0.2.5     readr_1.1.1    
 [9] tidyr_0.8.1     tibble_1.4.2    ggplot2_3.0.0   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.4  haven_1.1.2       lattice_0.20-35  
 [4] colorspace_1.3-2  htmltools_0.3.6   yaml_2.1.19      
 [7] rlang_0.2.1       R.oo_1.22.0       pillar_1.3.0     
[10] glue_1.3.0        withr_2.1.2       R.utils_2.6.0    
[13] modelr_0.1.2      readxl_1.1.0      bindr_0.1.1      
[16] plyr_1.8.4        munsell_0.5.0     gtable_0.2.0     
[19] cellranger_1.1.0  rvest_0.3.2       R.methodsS3_1.7.1
[22] evaluate_0.11     labeling_0.3      knitr_1.20       
[25] broom_0.5.0       Rcpp_0.12.18      scales_0.5.0     
[28] backports_1.1.2   jsonlite_1.5      hms_0.4.2        
[31] digest_0.6.15     stringi_1.2.4     grid_3.5.1       
[34] rprojroot_1.3-2   cli_1.0.0         tools_3.5.1      
[37] magrittr_1.5      lazyeval_0.2.1    crayon_1.3.4     
[40] whisker_0.3-2     pkgconfig_2.0.1   xml2_1.2.0       
[43] lubridate_1.7.4   assertthat_0.2.0  rmarkdown_1.10   
[46] httr_1.3.1        rstudioapi_0.7    R6_2.2.2         
[49] nlme_3.1-137      git2r_0.23.0      compiler_3.5.1

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Characterize orthologous peaks

Briana Mittleman

8/21/2018

Distance to ortho exon

Session information