Last updated: 2019-07-17

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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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File Version Author Date Message
html d48ec93 brimittleman 2019-07-16 Build site.
Rmd 67481df brimittleman 2019-07-16 frac spec anno and intron Pacbio
html fb1fde6 brimittleman 2019-07-16 Build site.
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

PacBio

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

intronic PAS

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