Read distribution Deep tools plots

Last updated: 2019-07-30

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Knit directory: apaQTL/analysis/

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Unstaged changes:
    Modified:   analysis/DiffIsoAnalysis.Rmd
    Modified:   analysis/NuclearSpecAPAqtl.Rmd
    Modified:   analysis/PASdescriptiveplots.Rmd
    Modified:   analysis/PrematureTermQTL.Rmd
    Modified:   analysis/QTLlocation.Rmd
    Modified:   analysis/chromHHMQTL.Rmd
    Modified:   analysis/compareAnnotatedpas.Rmd
    Modified:   analysis/nonNormQTL.Rmd
    Modified:   analysis/nucSpecinEQTLs.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/pQTLexampleplot.Rmd
    Modified:   analysis/propeQTLs_explained.Rmd
    Modified:   analysis/signalsiteanalysis.Rmd
    Modified:   code/BothFracDTPlotGeneRegions.sh
    Modified:   code/Snakefile
    Deleted:    code/Upstream10Bases_general.py
    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
    Deleted:    code/test.txt

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.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
Rmd	9384e8f	brimittleman	2019-07-30	change rna seq script
html	408f0b2	brimittleman	2019-05-22	Build site.
Rmd	498c964	brimittleman	2019-05-22	add plots as pngs
html	6952d4e	brimittleman	2019-05-21	Build site.
Rmd	54fb5e2	brimittleman	2019-05-21	add normalized plot code
html	e650e08	brimittleman	2019-04-22	Build site.
Rmd	851c963	brimittleman	2019-04-22	add reads against feature

In this analysis I will create the read distribution figures. These are created using deeptools. I have merged total and nuclear bam files from the read mapping pipeline. I will convert these to bigwigs in order to map the reads against features with deeptools.

Create BW files

mkdir ../data/mergedBW_byfrac
mkdir ../data/DTmatrix
mkdir ../output/dtPlots

module load Anaconda3 
source activate three-prime-env

sbatch bam2bw.sh ../data/mergedbyFracBam/Total.SamplesMerged.sort.bam ../data/mergedBW_byfrac/Total.SamplesMerged.bw 

sbatch bam2bw.sh ../data/mergedbyFracBam/Nuclear.SamplesMerged.sort.bam ../data/mergedBW_byfrac/Nuclear.SamplesMerged.bw

Map along gene bodies

sbatch BothFracDTPlotGeneRegions.sh

Redo with Normalized RPKM

I need to create normalized bw from each bam file. I then merge by fraction and convert back to bigwig from bedgraph.

I added a rule to the first snakefile that created the normalized files. Then I run the following to merge and create the bw.

sbatch mergeBW_norm.sh

Next I create the plot with deeptools.

sbatch BothFracDTPlotGeneRegions_normalized.sh

Same plots with RNA seq

I combined 6 samples of the Geuvadis RNA seq into one file for this.

sbatch RNAseqDTplot.sh

Zoom in on the TES

I will use the non normalized version of the merged bigwig and plot the 100bp up and downstream of annoated TES using bedtools. I will also do this in our RNA data.

BW total/nuclear: ../data/mergedBW_byfrac/Total.SamplesMerged.bw ../data/mergedBW_byfrac/Nuclear.SamplesMerged.bw

RNA: ../data/GeuvadisRNA/RNAseqGeuvadis_STAR_6samp_MergedBams.sort.bw

TES:
/project2/gilad/briana/genome_anotation_data/ncbiRefSeq_endProtCodGenes_sort.bed

sbatch TESplots100bp.sh
sbatch TESplots150bp.sh
sbatch TESplots200bp.sh

I want to only look at the first base in each read. This is the actual PAS. I can recompute the BW with the –Offset argument.

sbatch bam2BW_5primemost.sh ../data/mergedbyFracBam/Total.SamplesMerged.sort.bam ../data/mergedBW_byfrac/Total.SamplesMerged.5primemost.bw 

sbatch bam2BW_5primemost.sh ../data/mergedbyFracBam/Nuclear.SamplesMerged.sort.bam ../data/mergedBW_byfrac/Nuclear.SamplesMerged.5primemost.bw

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_1.4.0 Rcpp_1.0.0      digest_0.6.18   rprojroot_1.3-2
 [5] backports_1.1.2 git2r_0.25.2    magrittr_1.5    evaluate_0.12  
 [9] highr_0.7       stringi_1.2.4   fs_1.3.1        whisker_0.3-2  
[13] rmarkdown_1.10  tools_3.5.1     stringr_1.3.1   glue_1.3.0     
[17] yaml_2.2.0      compiler_3.5.1  htmltools_0.3.6 knitr_1.20