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
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Modified: code/makePheno.py
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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.
These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote
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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.
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
sbatch BothFracDTPlotGeneRegions.sh
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
I combined 6 samples of the Geuvadis RNA seq into one file for this.
sbatch RNAseqDTplot.sh
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