Last updated: 2020-02-02

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Unstaged changes:
    Modified:   analysis/LDregress.Rmd
    Modified:   analysis/NuclearSpecIncludeNotTested.Rmd
    Modified:   analysis/PASdescriptiveplots.Rmd
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/nucSpecinEQTLs.Rmd
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    Modified:   analysis/pQTLexampleplot.Rmd
    Modified:   analysis/propeQTLs_explained.Rmd
    Modified:   analysis/version15bpfilter.Rmd
    Modified:   code/DistPAS2Sig.py
    Modified:   code/apaQTLsnake.err
    Deleted:    code/test.txt
    Deleted:    reads_graphs.Rmd

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Rmd d0f4f33 brimittleman 2020-02-03 add TSS analysis

I will download encode cage data for TSS evidence in LCLs (GM12878). This cell line is a hapmap female of european ancestry. I will download the bed TSS file for HG19 for the nuclear fraction. I will also download the cytosolic fraction. This way I can ask if some of the isoforms in the nuclear specific overlap.

mkdir ../data/TSS

Nuclear file ENCFF358CEV.bed.gz There are 12344 peaks reported. Cytosolic file ENCFF140PCA.bed.gz There are 10991 peaks reported I will unzip and remove the chr.

gunzip ../data/TSS/ENCFF358CEV.bed.gz
sed 's/^chr//' ../data/TSS/ENCFF358CEV.bed >  ../data/TSS/ENCFF358CEV_Nuclear_noChr.bed
sort -k1,1  -k2,2n ../data/TSS/ENCFF358CEV_Nuclear_noChr.bed  > ../data/TSS/ENCFF358CEV_Nuclear_noChr.sort.bed


gunzip ../data/TSS/ENCFF140PCA.bed.gz
sed 's/^chr//' ../data/TSS/ENCFF140PCA.bed >  ../data/TSS/ENCFF140PCA_Cyto_noChr.bed
sort -k1,1 -k2,2n ../data/TSS/ENCFF140PCA_Cyto_noChr.bed > ../data/TSS/ENCFF140PCA_Cyto_noChr.sort.bed

I will look for nuclear specific TSS using bedtools.

-v in a not in b

bedtools intersect -v -a ../data/TSS/ENCFF358CEV_Nuclear_noChr.sort.bed -b  ../data/TSS/ENCFF140PCA_Cyto_noChr.sort.bed -s -sorted > CageSeq_NuclearSpecific.bed

There are 8049 TSS peaks in this set.


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     

loaded via a namespace (and not attached):
 [1] workflowr_1.5.0 Rcpp_1.0.2      digest_0.6.18   later_0.7.5    
 [5] rprojroot_1.3-2 R6_2.3.0        backports_1.1.2 git2r_0.26.1   
 [9] magrittr_1.5    evaluate_0.12   stringi_1.2.4   fs_1.3.1       
[13] promises_1.0.1  whisker_0.3-2   rmarkdown_1.10  tools_3.5.1    
[17] stringr_1.3.1   glue_1.3.0      httpuv_1.4.5    yaml_2.2.0     
[21] compiler_3.5.1  htmltools_0.3.6 knitr_1.20