Last updated: 2019-07-16

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Knit directory: apaQTL/analysis/

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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


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html fb1fde6 brimittleman 2019-07-16 Build site.
Rmd 2572d13 brimittleman 2019-07-16 add compare annotated and additional coverage

library(workflowr)
This is workflowr version 1.4.0
Run ?workflowr for help getting started
library(tidyverse)
── Attaching packages ─────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
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✔ readr   1.3.1       ✔ forcats 0.3.0  
── Conflicts ────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

I will se the annotated PAS from the Tian lab database (http://exon.umdnj.edu/polya_db/v3/misc/download.php)

mkdir ../data/AnnotatedPAS/
  
#file =human.PAS.txt

I want to make this into a file I can overlap with my PAS. In order to know what resolution I should use for calling a PAS the same, I will look for the closest annotated PAS to each of my sites. To do this I will need to create a bed file with these.

python annotatedPAS2bed.py
sort -k1,1 -k2,2n ../data/AnnotatedPAS/human.PAS.bed > ../data/AnnotatedPAS/human.PAS.sort.bed

sbatch closestannotated.sh
dist=read.table("../data/AnnotatedPAS/DistanceMyPAS2Anno.bed", col.names = c("chr", "start","end","myPAS", "score","strand","chr2", "start2", "end2", "anno", "score2", "strand2", "distance"),stringsAsFactors = F)

Plot the distance.

ggplot(dist,aes(x=distance))+ geom_histogram(bins=300) + xlim(-25, 25)
Warning: Removed 20495 rows containing non-finite values (stat_bin).

Version Author Date
fb1fde6 brimittleman 2019-07-16

Looks like about 10 basepairs is ok resolution. I need to make sure these map 1 to 1 when you filter these.

PAS_withmatch=dist %>% filter(abs(distance)<=10) %>% select(myPAS,anno) %>% unique() %>% separate(myPAS, into=c("pasNum", "geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc"), sep="_")

ggplot(PAS_withmatch,aes(x=loc)) + geom_histogram(stat="count")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Version Author Date
fb1fde6 brimittleman 2019-07-16

I want to look at those I find that they do not.

allMyPAS=read.table("../data/PAS/APAPAS_GeneLocAnno.5perc.sort.bed",stringsAsFactors = F, col.names = c("chr","start","end", "PASID", "score","strand"))  %>% separate(PASID, into=c("pasNum", "geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc"), sep="_") %>% mutate(withAnno=ifelse(pasNum %in% PAS_withmatch$pasNum, "Yes","No"))

PASnoMatch=allMyPAS %>% anti_join(PAS_withmatch,by="pasNum")
ggplot(allMyPAS,aes(x=loc,fill=withAnno)) + geom_histogram(stat="count") + labs(title = "PAS by annotated PAS within 10bp") +scale_fill_brewer(palette = "Dark2")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Version Author Date
fb1fde6 brimittleman 2019-07-16

Look at total and nuclear seperatly.

python NuclearPAS_5per.bed.py


python TotalPAS_5perc.bed.py
sort -k1,1 -k2,2n ../data/PAS/APApeak_Peaks_GeneLocAnno.Nuclear.5perc.bed > ../data/PAS/APApeak_Peaks_GeneLocAnno.Nuclear.5perc.sort.bed

sort -k1,1 -k2,2n ../data/PAS/APApeak_Peaks_GeneLocAnno.Total.5perc.bed > ../data/PAS/APApeak_Peaks_GeneLocAnno.Total.5perc.sort.bed

Run the distance script with these.

sbatch closestannotated_byfrac.sh

Total

Totaldist=read.table("../data/AnnotatedPAS/Total_DistanceMyPAS2Anno.bed", col.names = c("chr", "start","end","myPAS", "score","strand","chr2", "start2", "end2", "anno", "score2", "strand2", "distance"),stringsAsFactors = F)

ggplot(Totaldist,aes(x=distance))+ geom_histogram(bins=300) + xlim(-25, 25)
Warning: Removed 13578 rows containing non-finite values (stat_bin).

Totaldist_withAnno=Totaldist %>% filter(abs(distance)<=10) %>% select(myPAS,anno) %>% unique() %>% separate(myPAS, into=c("pasNum", "geneID", "loc"), sep=":")

allTotalPAS=read.table("../data/PAS/APApeak_Peaks_GeneLocAnno.Total.5perc.sort.bed",stringsAsFactors = F, col.names = c("chr","start","end", "PASID", "score","strand"))  %>% separate(PASID, into=c("pasNum", "geneID", "loc"), sep=":") %>% mutate(withAnno=ifelse(pasNum %in% Totaldist_withAnno$pasNum, "Yes","No"))
ggplot(allTotalPAS,aes(x=loc,fill=withAnno)) + geom_histogram(stat="count") + labs(title = "TotalPAS by annotated PAS within 10bp") +scale_fill_brewer(palette = "Dark2")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Nuclear

Nucleardist=read.table("../data/AnnotatedPAS/Nuclear_DistanceMyPAS2Anno.bed", col.names = c("chr", "start","end","myPAS", "score","strand","chr2", "start2", "end2", "anno", "score2", "strand2", "distance"),stringsAsFactors = F)

ggplot(Nucleardist,aes(x=distance))+ geom_histogram(bins=300) + xlim(-25, 25)
Warning: Removed 19400 rows containing non-finite values (stat_bin).

Nucleardist_withAnno=Nucleardist %>% filter(abs(distance)<=10) %>% select(myPAS,anno) %>% unique() %>% separate(myPAS, into=c("pasNum", "geneID", "loc"), sep=":")

allNuclearPAS=read.table("../data/PAS/APApeak_Peaks_GeneLocAnno.Nuclear.5perc.sort.bed",stringsAsFactors = F, col.names = c("chr","start","end", "PASID", "score","strand"))  %>% separate(PASID, into=c("pasNum", "geneID", "loc"), sep=":") %>% mutate(withAnno=ifelse(pasNum %in% Nucleardist_withAnno$pasNum, "Yes","No"))
ggplot(allNuclearPAS,aes(x=loc,fill=withAnno)) + geom_histogram(stat="count") + labs(title = "Nuclear PAS by annotated PAS within 10bp") +scale_fill_brewer(palette = "Dark2")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Nuclear specific:

NuclearSpec=allNuclearPAS %>% anti_join(allTotalPAS,by = "pasNum")

ggplot(NuclearSpec,aes(x=loc,fill=withAnno)) + geom_histogram(stat="count") + labs(title = "Nuclear  Specific PAS by annotated PAS within 10bp") +scale_fill_brewer(palette = "Dark2")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Total Specific:

TotalSpec=allTotalPAS %>% anti_join(allNuclearPAS,by = "pasNum")

ggplot(TotalSpec,aes(x=loc,fill=withAnno)) + geom_histogram(stat="count") + labs(title = "Total  Specific PAS by annotated PAS within 10bp") +scale_fill_brewer(palette = "Dark2")
Warning: Ignoring unknown parameters: binwidth, bins, pad


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] forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1   purrr_0.3.2    
 [5] readr_1.3.1     tidyr_0.8.3     tibble_2.1.1    ggplot2_3.1.1  
 [9] tidyverse_1.2.1 workflowr_1.4.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0         RColorBrewer_1.1-2 cellranger_1.1.0  
 [4] plyr_1.8.4         compiler_3.5.1     pillar_1.3.1      
 [7] git2r_0.25.2       highr_0.7          tools_3.5.1       
[10] digest_0.6.18      lubridate_1.7.4    jsonlite_1.6      
[13] evaluate_0.12      nlme_3.1-137       gtable_0.2.0      
[16] lattice_0.20-38    pkgconfig_2.0.2    rlang_0.4.0       
[19] cli_1.1.0          rstudioapi_0.10    yaml_2.2.0        
[22] haven_1.1.2        withr_2.1.2        xml2_1.2.0        
[25] httr_1.3.1         knitr_1.20         hms_0.4.2         
[28] generics_0.0.2     fs_1.3.1           rprojroot_1.3-2   
[31] grid_3.5.1         tidyselect_0.2.5   glue_1.3.0        
[34] R6_2.3.0           readxl_1.1.0       rmarkdown_1.10    
[37] modelr_0.1.2       magrittr_1.5       whisker_0.3-2     
[40] backports_1.1.2    scales_1.0.0       htmltools_0.3.6   
[43] rvest_0.3.2        assertthat_0.2.0   colorspace_1.3-2  
[46] labeling_0.3       stringi_1.2.4      lazyeval_0.2.1    
[49] munsell_0.5.0      broom_0.5.1        crayon_1.3.4