Last updated: 2020-02-09

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Unstaged changes:
    Modified:   analysis/ExploreNpas.Rmd
    Modified:   analysis/NuclearSpecIncludeNotTested.Rmd
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    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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File Version Author Date Message
Rmd 0ea6bf8 brimittleman 2020-02-10 add mirna disrupt analysis

In this analysis I will test if any of the QTLs distrupt conserved miRNA binding sites in conserved miRNA families. I will do this with a bed intersection starting with the QTLs.

sed 's/^chr//' ../data/miRNAbinding/Targets_CS_pctiles.hg19.consFam.consSite.bed > ../data/miRNAbinding/Targets_CS_pctiles.hg19.consFam.consSite.NoChr.bed


sed '1d'  ../data/apaQTLs/Nuclear_apaQTLs4pc_5fdr.WITHSTRAND.bed | sort -k1,1 -k2,2n >  ../data/apaQTLs/Nuclear_apaQTLs4pc_5fdr.WITHSTRAND.sort.bed 
sed '1d'   ../data/apaQTLs/Total_apaQTLs4pc_5fdr.WITHSTRAND.bed  | sort -k1,1 -k2,2n > ../data/apaQTLs/Total_apaQTLs4pc_5fdr.WITHSTRAND.sort.bed 


sbatch miRNAdisrupt.sh

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