Last updated: 2019-09-07

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Knit directory: apaQTL/analysis/

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Unstaged changes:
    Modified:   analysis/NuclearSpecIncludeNotTested.Rmd
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/compareAnnotatedpas.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/signalsiteanalysis.Rmd
    Modified:   analysis/version15bpfilter.Rmd
    Modified:   code/BothFracDTPlotGeneRegions.sh
    Modified:   code/Snakefile
    Modified:   code/SnakefilefiltPAS
    Modified:   code/apaQTLCorrectPvalMakeQQ.R
    Modified:   code/apaQTL_Nominal.sh
    Modified:   code/apaQTL_permuted.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/bam2bw.sh
    Modified:   code/bed2saf.py
    Modified:   code/cluster.json
    Modified:   code/clusterfiltPAS.json
    Modified:   code/config.yaml
    Modified:   code/environment.yaml
    Modified:   code/makePheno.py
    Modified:   code/mergeAllBam.sh
    Modified:   code/mergeByFracBam.sh
    Modified:   code/mergePeaks.sh
    Modified:   code/peakFC.sh
    Modified:   code/snakemake.batch
    Modified:   code/snakemakePAS.batch
    Modified:   code/snakemakefiltPAS.batch
    Modified:   code/submit-snakemake.sh
    Modified:   code/submit-snakemakePAS.sh
    Modified:   code/submit-snakemakefiltPAS.sh
    Deleted:    code/test.txt
    Modified:   data/MetaDataSequencing.txt
    Deleted:    reads_graphs.Rmd

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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Rmd c5c6546 brimittleman 2019-09-07 add enrichment analysis

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()

In this analysis I will look at the enrichment of 3’ UTR pas over all PAS. I need to get the size of all UTR regions and the size of all regions. I can do this by merging the annotations.

I can use bedtools merge on

ncbiRefSeq_FormatedallAnnotation.sort.bed and the UTR 3 regions of this.

annotation=read.table("/project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefSeq_FormatedallAnnotation.sort.bed", col.names = c("chr", "start", "end", "id", "score", "strand")) %>% separate(id,into=c("loc", "gene"),sep=":")

utr3=annotation %>% filter(loc=="utr3") 

write.table(utr3, "/project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefSeq_UTR3.bed", col.names = F, row.names = F,quote = F, sep="\t")

sort:

sort -k1,1 -k2,2n /project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefseq_3UTR.dms > /project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefseq_3UTR.sort.bed

sed 's/^chr//' /project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefseq_3UTR.sort.bed > /project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefseq_3UTR.sort.noCHR.bed
sbatch mergeAnnotations.sh
chroms=as.character(seq(1,22))

utrMerged=read.table("/project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefSeq_Merged_UTR3.sort.bed",col.names = c("chr", "start", "end")) %>% mutate(length=end-start) %>% filter(chr %in% chroms)
allMerged=read.table("/project2/gilad/briana/genome_anotation_data/RefSeq_annotations/ncbiRefSeq_Merged.FormatedallAnnotation.sort.bed" , col.names = c("chr", "start", "end")) %>% mutate(length=end-start) %>% filter(chr %in% chroms)
totalLength=sum(allMerged$length)
utrLength=sum(utrMerged$length)

N pas in UTR3

utr3pas=read.table("../data/PAS/APAPAS_GeneLocAnno.5perc.bed", col.names = c("chr", "start", "end", "id","score", "strand")) %>% separate(id, into = c("pasnum", "geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc"),sep="_") %>% filter(loc=="utr3")
allPAS=read.table("../data/PAS/APAPAS_GeneLocAnno.5perc.bed")

Values:

pas_length=nrow(allPAS)/totalLength
utr_length=nrow(utr3pas)/utrLength 


enrichment=utr_length/pas_length
enrichment
[1] 19.43483

This is a 19.43 enrichment.


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

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        workflowr_1.4.0 
 [9] tools_3.5.1      digest_0.6.18    lubridate_1.7.4  jsonlite_1.6    
[13] evaluate_0.12    nlme_3.1-137     gtable_0.2.0     lattice_0.20-38 
[17] pkgconfig_2.0.2  rlang_0.4.0      cli_1.1.0        rstudioapi_0.10 
[21] yaml_2.2.0       haven_1.1.2      withr_2.1.2      xml2_1.2.0      
[25] httr_1.3.1       knitr_1.20       hms_0.4.2        generics_0.0.2  
[29] fs_1.3.1         rprojroot_1.3-2  grid_3.5.1       tidyselect_0.2.5
[33] glue_1.3.0       R6_2.3.0         readxl_1.1.0     rmarkdown_1.10  
[37] modelr_0.1.2     magrittr_1.5     whisker_0.3-2    backports_1.1.2 
[41] scales_1.0.0     htmltools_0.3.6  rvest_0.3.2      assertthat_0.2.0
[45] colorspace_1.3-2 stringi_1.2.4    lazyeval_0.2.1   munsell_0.5.0   
[49] broom_0.5.1      crayon_1.3.4