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workflow.txt
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workflow.txt
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### This workflow has to be sequentially ran to obtain the results from our manuscript. Be aware that some steps can take a very long time, or need changes regarding the number of processors available. BASEDIR has to be adapted to your local directory.
conda env create -f saseRPaper.yml
conda env create -f rsem.1.3.0.yml
conda env create -f Fraser.2.0.yml
conda env create -f leafcutter.yml
BASEDIR=/data/gent/vo/000/gvo00063/Alex/saseRPaper
FUNCTIONDIR=$BASEDIR/R-Functions
RUNNINGSCRIPTDIR=$BASEDIR/Running-scripts
DATADIR=$BASEDIR/Data
GTEx=$DATADIR/GTEx
GEUVADIS=$DATADIR/Geuvadis
KREMER=$DATADIR/Kremer
ABERRANTEXPRESSION=$BASEDIR/Aberrant-expression
DIFFERENTIALUSAGE=$BASEDIR/Differential-usage
ABERRANTSPLICING=$BASEDIR/Aberrant-splicing
FIGURESDIR=$BASEDIR/Figures
LEAFCUTTERFUNC=$BASEDIR/leafcutter
# Downloading data ----------------------------------------------------------------------
## GTEx
conda activate saseRPaper
cd $GTEx
wget https://storage.googleapis.com/gtex_analysis_v6p/rna_seq_data/GTEx_Analysis_v6p_RNA-seq_RNA-SeQCv1.1.8_gene_reads.gct.gz
wget https://storage.googleapis.com/gtex_analysis_v6p/annotations/GTEx_Data_V6_Annotations_SampleAttributesDD.xlsx ;
wget https://storage.googleapis.com/gtex_analysis_v6p/reference/gencode.v19.genes.v6p_model.patched_contigs.gtf.gz
wget https://storage.googleapis.com/gtex_analysis_v6p/annotations/GTEx_Data_V6_Annotations_SampleAttributesDS.txt
wget https://storage.googleapis.com/gtex_analysis_v6p/annotations/GTEx_Data_V6_Annotations_SubjectPhenotypesDS.txt
gunzip GTEx_Analysis_v6p_RNA-seq_RNA-SeQCv1.1.8_gene_reads.gct.gz
gunzip gencode.v19.genes.v6p_model.patched_contigs.gtf.gz
cd $BASEDIR
R --no-save --no-restore-data -e "rmarkdown::render('GTEx_data_preparation.Rmd')" "--args data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
python
import pandas as pd
df = pd.read_csv("./Data/GTEx/GTEx_counts_Marginal_Outliers.csv")
df_renamed = df.rename(index = df["Unnamed: 0"])
df_final = df_renamed.drop(columns = "Unnamed: 0")
df_final.to_csv("./Data/GTEx/GTEx_counts_Marginal_Outliers_pandasdf.csv",index = True, header = True)
exit()
## Kremer
cd $KREMER
### Kremer dataset download: https://static-content.springer.com/esm/art%3A10.1038%2Fncomms15824/MediaObjects/41467_2017_BFncomms15824_MOESM390_ESM.txt
### Metadata Kremer download: https://static-content.springer.com/esm/art%3A10.1038%2Fncomms15824/MediaObjects/41467_2017_BFncomms15824_MOESM397_ESM.txt
### Kremer mapping requires local running of DATAPREPDIR/Kremer_mapping.Rmd
curl "https://zenodo.org/record/4271599/files/kremer--hg19--gencode34.tar.gz?download=1" --output kremer--hg19--gencode34.tar.gz #version 3!
gunzip kremer--hg19--gencode34.tar.gz
tar -xvf kremer--hg19--gencode34.tar
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh37_mapping/gencode.v34lift37.annotation.gtf.gz
cd $BASEDIR
R --no-save --no-restore-data -e "rmarkdown::render('$Kremer/Kremer_data_preparation_aberrant_expression.Rmd')" "--args data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$KREMER/Kremer_data_preparation_aberrant_splicing.Rmd')" "--args data_directory='$DATADIR'"
conda activate Fraserjaccard
R --no-save --no-restore-data -e "rmarkdown::render('$KREMER/Kremer_data_preparation_aberrant_splicing_jaccard.Rmd')" "--args data_directory='$DATADIR'"
conda activate saseRPaperaper
python
import pandas as pd
df = pd.read_csv("./Data/Kremer/Kremer_counts.csv")
df_renamed = df.rename(index = df["Unnamed: 0"])
df_final = df_renamed.drop(columns = "Unnamed: 0")
df_final.to_csv("./Data/Kremer/Kremer_counts_pandasdf.csv",index = True, header = True)
exit()
python
import pandas as pd
df = pd.read_csv("./Data/Kremer/Kremer_counts_Marginal_Outliers.csv")
df_renamed = df.rename(index = df["Unnamed: 0"])
df_final = df_renamed.drop(columns = "Unnamed: 0")
df_final.to_csv("./Data/Kremer/Kremer_counts_Marginal_Outliers_pandasdf.csv",index = True, header = True)
exit()
## Geuvadis
cd $GEUVADIS
cd fastq-files
for i in {23..62}; do fastq-dump --split-3 ERR1880${i}; done
cd ../Annotation
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.primary_assembly.annotation.gtf.gz
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/GRCh38.primary_assembly.genome.fa.gz
gunzip gencode.v42.primary_assembly.annotation.gtf.gz
gunzip GRCh38.primary_assembly.genome.fa.gz
grep -v "^H" gencode.v42.primary_assembly.annotation.gtf \
> gencode.v42.primary_assembly.annotation_filter.gtf
grep "protein_coding" gencode.v42.primary_assembly.annotation_filter.gtf \
> Homo_sapiens.GRCh38.42.primary_assembly.protein_coding.gtf
cd $BASEDIR
conda activate rsem.1.3.0 # change to use rsem
rsem-prepare-reference \
--gtf $GEUVADIS/Annotation/Homo_sapiens.GRCh38.42.primary_assembly.protein_coding.gtf --star -p 16 \
$GEUVADIS/Annotation/GRCh38.primary_assembly.genome.fa \
$GEUVADIS/Annotation/Homo_sapiens.GRCh38.42
cd $GEUVADIS/Calculated_expression
for i in {23..62}; do \
mkdir ERR1880$i ;\
rsem-calculate-expression \
--paired-end -p 20 --star --seed 1$i \
$GEUVADIS/fastq-files/ERR1880${i}_1.fastq $GEUVADIS/fastq-files/ERR1880${i}_2.fastq \
$GEUVADIS/Annotation/Homo_sapiens.GRCh38.42 \
ERR1880${i}/ERR1880${i} ;\
done
conda activate saseRPaper
cd $BASEDIR
for i in {23..62}; do \
Sample=ERR1880${i} ;\
R --no-save --no-restore-data -e "rmarkdown::render('$GEUVADIS/Aberrant-splicing-outlier-injection.Rmd')" \
"--args data_directory='$GEUVADIS/Calculated_expression/$Sample' sample='$Sample' output_dir='$GEUVADIS/Calculated_expression/$Sample' freq=0.001" ;\
done
conda activate rsem.1.3.0 # change to use rsem
cd $GEUVADIS
for i in {23..62}; do \
cd Calculated_expression/ERR1880${i} ;\
sed -n '1p' ERR1880${i}.stat/ERR1880${i}.cnt | sed 's/|/ /' | awk '{print $4}' > libary_size.txt ;\
sed -n '3p' ERR1880${i}.stat/ERR1880${i}.theta | sed 's/|/ /' | awk '{print $1}' > theta_0.txt ;\
library_size=$(<libary_size.txt) ;\
theta_0=$(<theta_0.txt) ;\
cd ../.. ;\
rsem-simulate-reads \
Annotation/Homo_sapiens.GRCh38.42 \
Calculated_expression/ERR1880${i}/ERR1880${i}.stat/ERR1880${i}.model \
Calculated_expression/ERR1880${i}/ERR1880${i}_generation_details.txt \
$theta_0 $library_size Calculated_expression/ERR1880${i}/simulated_reads_ERR1880${i} --seed 1${i} ;\
done
cd $BASEDIR
STAR --runThreadN 16 --runMode genomeGenerate --genomeDir $GEUVADIS/Annotation/STAR_Annotation/ \
--genomeFastaFiles $GEUVADIS/Annotation/GRCh38.primary_assembly.genome.fa \
--sjdbGTFfile $GEUVADIS/Annotation/Homo_sapiens.GRCh38.42.primary_assembly.protein_coding.gtf
for i in {23..62}; do \
STAR --runThreadN 1 --genomeDir $GEUVADIS/Annotation/STAR_Annotation \
--outSAMtype BAM SortedByCoordinate \
--sjdbGTFfile $GEUVADIS/Annotation/Homo_sapiens.GRCh38.42.primary_assembly.protein_coding.gtf \
--sjdbOverhang 100 --readFilesIn $GEUVADIS/Calculated_expression/ERR1880${i}/simulated_reads_ERR1880${i}_1.fq $GEUVADIS/Calculated_expression/ERR1880${i}/simulated_reads_ERR1880${i}_2.fq \
--quantMode TranscriptomeSAM GeneCounts --outFileNamePrefix $GEUVADIS/Calculated_expression/ERR1880${i}/simulated_star_alignment_ERR1880${i} ;\
done
for i in {23..62}; do \
samtools index $GEUVADIS/Calculated_expression/ERR1880${i}/simulated_star_alignment_ERR1880${i}Aligned.sortedByCoord.out.bam $GEUVADIS/Calculated_expression/ERR1880${i}/simulated_star_alignment_ERR1880${i}Aligned.sortedByCoord.out.bam.bai ;\
done
conda activate saseRPaper
R --no-save --no-restore-data -e "rmarkdown::render('$GEUVADIS/ASpli_genome_binning.Rmd')" \
"--args outputdir='$GEUVADIS/Annotation/features.RDS' cores=10 gtfdir='$GEUVADIS/Annotation/Homo_sapiens.GRCh38.42.primary_assembly.protein_coding.gtf'"
R --no-save --no-restore-data -e "rmarkdown::render('$GEUVADIS/Bam_to_ASpli_counts.Rmd')" \
"--args outputdir='$GEUVADIS/ASpli-counts.RDS' datadir='$GEUVADIS' cores=MulticoreParam(workers=10) featuresdir='$GEUVADIS/Annotation/features.RDS' functiondir='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$GEUVADIS/Bam_to_Fraser_counts.Rmd')" \
"--args datadir='$GEUVADIS' cores=MulticoreParam(workers=10)"
R --no-save --no-restore-data -e "rmarkdown::render('$GEUVADIS/Outlier-gene-matrix-formation.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$GEUVADIS'"
## SatuRn data
cd $DIFFERENTIALUSAGE/Data
curl "https://zenodo.org/record/6826603/files/Performance_GTEx.zip?download=1" --output Performance_GTEx.zip
curl "https://zenodo.org/record/6826603/files/Scalability_data.zip?download=1" --output Scalability_analysis.zip
curl "https://zenodo.org/record/6826603/files/Performance_Chen.zip?download=1" --output Performance_Chen.zip
curl "https://zenodo.org/record/6826603/files/Performance_Hsapiens.zip?download=1" --output Performance_Hsapiens.zip
unzip Performance_GTEx.zip
unzip Scalability_analysis.zip
unzip Performance_Chen.zip
unzip Performance_Hsapiens.zip
mv GTEx/GTEx_benchmark_datasets_count.Rdata ./
mv Chen/Chen_benchmark_datasets_count.Rdata ./
mv Chen/Chen_metadata.csv ./
mv Performance_Hsapiens/Hsapiens_benchmark_datasets_count.Rdata ./
mv Performance_Hsapiens/Hsapiens_metadata_1.txt ./
mv Scalability_data/quantsf_counts_bulk.Rds ./
mv Scalability_data/tx2gene_bulk.Rds ./
# Aberrant expression -------------------------------------------------------------------
## Kremer
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script_optimalThreshold.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_optimalThreshold_Analysis_Kremer_Marginal_outliers.RDS' design=~1 cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_autoencoder_Analysis_Kremer_Marginal_outliers.RDS' autoencoder='autoencoder' cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_PCA_Analysis_Kremer_Marginal_outliers.RDS' autoencoder='pca' cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Kremer_Marginal_outliers.RDS' design=~1 cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_edgeR_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_edgeR_Analysis_Kremer_Marginal_outliers.RDS' cores=MulticoreParam(workers=1)"
(time python $FUNCTIONDIR/outsingle/fast_zscore_estimation.py $KREMER/Kremer_counts_Marginal_Outliers_pandasdf.csv && time python $FUNCTIONDIR/outsingle/optht_svd_zs.py $KREMER/Kremer_counts_Marginal_Outliers_pandasdf-fzse-zs.csv) > ./Aberrant-expression/Output_files/time_OutSingle_Kremer_Marginal_Outliers.txt 2>&1
mv $KREMER/Kremer_counts_Marginal_Outliers_pandasdf-fzse-zs-svd-optht-zs.csv ./Aberrant-expression/Output_files/Kremer_counts_Marginal_Outliers_pandasdf-fzse-zs-svd-optht-zs.csv
(time python $FUNCTIONDIR/outsingle/fast_zscore_estimation.py $KREMER/Kremer_counts_Marginal_Outliers_pandasdf.csv && time python $FUNCTIONDIR/outsingle/optht_svd_zs.py $KREMER/Kremer_counts_Marginal_Outliers_pandasdf-fzse-zs.csv) > ./Aberrant-expression/Output_files/time_OutSingle_Kremer_Marginal_Outliers_testingttt.txt 2>&1
## GTEx
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script_optimalThreshold.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_optimalThreshold_Analysis_GTEx_Marginal_outliers.RDS' design=~1 cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_edgeR_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_edgeR_Analysis_GTEx_Marginal_outliers.RDS' cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_GTEx_Marginal_outliers.RDS' design=~1 cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_PCA_Analysis_GTEx_Marginal_outliers.RDS' autoencoder='pca' cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_analysis_script_in_parts.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_autoencoder_Analysis_GTEx_Marginal_outliers_in_parts_1.RDS' autoencoder='autoencoder' cores=MulticoreParam(workers=1) params=seq(2,50,2)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_analysis_script_in_parts.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_autoencoder_Analysis_GTEx_Marginal_outliers_in_parts_2.RDS' autoencoder='autoencoder' cores=MulticoreParam(workers=1) params=seq(52,100,2)"
(time python $FUNCTIONDIR/outsingle/fast_zscore_estimation.py $GTEx/GTEx_counts_Marginal_Outliers_pandasdf.csv && time python $FUNCTIONDIR/outsingle/optht_svd_zs.py $GTEx/GTEx_counts_Marginal_Outliers_pandasdf-fzse-zs.csv) > ./Aberrant-expression/Output_files/time_OutSingle.txt 2>&1
mv $GTEx/GTEx_counts_Marginal_Outliers_pandasdf-fzse-zs-svd-optht-zs.csv ./Aberrant-expression/Output_files/GTEx_counts_Marginal_Outliers_pandasdf-fzse-zs-svd-optht-zs.csv
## Covariate specific
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Conditional_Outliers_Ischemic_time.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Conditional_outliers_Ischemic_time.RDS' design=~1 cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Conditional_Outliers_Sex.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Conditional_outliers_Sex_with_covariates.RDS' design=~SEX cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Conditional_Outliers_Ischemic_time.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Conditional_outliers_Ischemic_time_with_covariates.RDS' design=~DEATH cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Conditional_Outliers_Sex.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Conditional_outliers_Sex.RDS' design=~1 cores=MulticoreParam(workers=1)"
## Case study
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script_optimalThreshold.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_optimalThreshold_Analysis_Case_study.RDS' design=~1 cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Case_study.RDS' design=~1 cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_PCA_Analysis_Case_study.RDS' autoencoder='pca' cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_analysis_script.Rmd')" \
"--args data_directory='$DATADIR/Kremer/Kremer_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_PCA_Analysis_Kremer_Marginal_outliers.RDS' autoencoder='pca' cores=MulticoreParam(workers=1)"
(time python $FUNCTIONDIR/outsingle/fast_zscore_estimation.py $KREMER/Kremer_counts_pandasdf.csv && time python $FUNCTIONDIR/outsingle/optht_svd_zs.py $KREMER/Kremer_counts_pandasdf-fzse-zs.csv) > ./Aberrant-expression/Output_files/time_OutSingle_Kremer_Disease.txt 2>&1
mv $KREMER/Kremer_counts_pandasdf-fzse-zs-svd-optht-zs.csv ./Aberrant-expression/Output_files/Kremer_counts_pandasdf-fzse-zs-svd-optht-zs.csv
## Computational benchmarks
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_edgeR_Computational_time_latent_factors.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_edgeR_Analysis_Computational_time_confounders_5-160.RDS' number_of_confounders=seq(5,160,5) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_edgeR_Computational_time_latent_factors.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_edgeR_Analysis_Computational_time_confounders_165-200.RDS' number_of_confounders=seq(165,200,5) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_Computational_time_latent_factors.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_autoencoder_Analysis_Computational_time_confounders_1.RDS' autoencoder='autoencoder' number_of_confounders=seq(5,100,5) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_Computational_time_latent_factors.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_autoencoder_Analysis_Computational_time_confounders_2.RDS' autoencoder='autoencoder' number_of_confounders=seq(105,200,5) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_Computational_time_latent_factors.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_PCA_Analysis_Computational_time_confounders.RDS' autoencoder='pca' number_of_confounders=seq(5,200,5) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_Computational_time_latent_factors.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Computational_time_confounders.RDS' number_of_confounders=seq(5,200,5) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_edgeR_Computational_time_number_genes.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_edgeR_Analysis_Computational_time_genes.RDS' number_of_genes=seq(1000,17000,1000) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_Computational_time_number_genes.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Computational_time_genes.RDS' number_of_genes=seq(1000,17000,1000) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_Computational_time_number_genes.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_PCA_Analysis_Computational_time_genes.RDS' autoencoder='pca' number_of_genes=seq(1000,17000,1000) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_Computational_time_number_genes.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_autoencoder_Analysis_Computational_time_genes.RDS' autoencoder='autoencoder' number_of_genes=seq(1000,17000,1000) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_edgeR_Computational_time_number_patients.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_edgeR_Analysis_Computational_time_patients.RDS' number_of_patients=seq(60,220,20) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/RUV_Computational_time_number_patients.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/RUV_Analysis_Computational_time_patients.RDS' number_of_patients=seq(60,220,20) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_Computational_time_number_patients.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_autoencoder_Analysis_Computational_time_patients.RDS' autoencoder='autoencoder' number_of_patients=seq(60,220,20) cores=MulticoreParam(workers=1)"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTEXPRESSION/Outrider_Computational_time_number_patients.Rmd')" \
"--args data_directory='$DATADIR/GTEx/GTEx_counts_Marginal_Outliers.RDS' function_directory='$FUNCTIONDIR' output_directory='$ABERRANTEXPRESSION/Output_files/Outrider_PCA_Analysis_Computational_time_patients.RDS' autoencoder='pca' number_of_patients=seq(60,220,20) cores=MulticoreParam(workers=1)"
# Differential splicing
cd $BASEDIR/Differential-usage/Scalability_benchmark
./runtime
cd $BASEDIR
R --no-save --no-restore-data -e "rmarkdown::render('$BASEDIR/Differential-usage/Performance_benchmarks/Gtex_DTU.Rmd')"
R --no-save --no-restore-data -e "rmarkdown::render('$BASEDIR/Differential-usage/Performance_benchmarks/Hsapiens_DTU.Rmd')"
R --no-save --no-restore-data -e "rmarkdown::render('$BASEDIR/Differential-usage/Performance_benchmarks/Chen_DTU.Rmd')"
# Aberrant splicing
## Geuvadis
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-threshold-Bins-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-threshold-Junctions-genes-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-threshold-Junctions-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-threshold-jaccard-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' function_directory='$FUNCTIONDIR' annotation_directory='$GEUVADIS/Annotation'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-Bins-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-Junctions-genes-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-Junctions-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-jaccard-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' function_directory='$FUNCTIONDIR' annotation_directory='$GEUVADIS/Annotation'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-full-Analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-BB-Decoder-Analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-AE-weighted-Analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
conda activate leafcutter
for i in {23..62}; do
bamfile=$GEUVADIS/Calculated_expression/ERR1880${i}/simulated_star_alignment_ERR1880${i}Aligned.sortedByCoord.out.bam
bedfile=$bamfile.bed
juncfile=$bamfile.junc
samtools view $bamfile | python $LEAFCUTTERFUNC/scripts/filter_cs.py | $LEAFCUTTERFUNC/scripts/sam2bed.pl --use-RNA-strand - $bedfile
$LEAFCUTTERFUNC/scripts/bed2junc.pl $bedfile $juncfile
rm $bedfile
echo $bamfile.junc >> $LEAFCUTTERFUNC/output/juncfiles_leafcutter.txt ;
done
python $LEAFCUTTERFUNC/clustering/leafcutter_cluster.py -j $LEAFCUTTERFUNC/output/juncfiles_leafcutter.txt -m 15 -o $LEAFCUTTERFUNC/output/leafcutter-clustering/leafcutter-clustering -l 500000 –checkchrom
leafcutter/scripts/leafcutterMD.R --num_threads 8 leafcutter/output/leafcutter-clustering/leafcutter-clustering_perind_numers.counts.gz
mv leafcutter_outlier_clusterPvals.txt leafcutter/output/
mv leafcutter_outlier_effSize.txt leafcutter/output/
mv leafcutter_outlier_pVals.txt leafcutter/output/
cd leafcutter
mv simulated_star_alignment_ERR1880* output
leafviz/gtf2leafcutter.pl -o $GEUVADIS/Annotation/leafcutterannotation $GEUVADIS/Annotation/Homo_sapiens.GRCh38.42.primary_assembly.protein_coding.gtf
cd $BASEDIR
R --no-save --no-restore-data -e "rmarkdown::render('$LEAFCUTTERFUNC/Leafcutter_results_processing.Rmd')" \
"--args data_directory='$LEAFCUTTERFUNC/output' annotation_directory='$GEUVADIS/Annotation' output_directory='$ABERRANTSPLICING/Output_files'"
cd SPOT
python spot.py --juncfile $LEAFCUTTERFUNC/output/leafcutter-clustering/leafcutter-clustering_perind_numers.counts.gz --outprefix SPOT_results_
cd $BASEDIR
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/SPOT_results_processing.Rmd')" \
"--args data_directory='$BASEDIR/SPOT' annotation_directory='$GEUVADIS/Annotation' output_directory='$ABERRANTSPLICING/Output_files'"
conda activate Fraserjaccard
cd $ABERRANTSPLICING
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-jaccard-full-Analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-Jaccard-BB-Decoder-Analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-Jaccard-AE-weighted-Analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
## Kremer Jaccard outliers
conda activate saseRPaper
cd $BASEDIR
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-threshold-Junctions-genes-full-analysis-Kremer-jaccard-outliers.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-threshold-jaccard-analysis-Kremer-jaccard-outliers.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-Junctions-genes-full-analysis-Kremer-jaccard-outliers.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-jaccard-analysis-Kremer-jaccard-outliers.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-full-Analysis-jaccard-outliers-psi5.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-full-Analysis-jaccard-outliers-psi3.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-AE-Analysis-jaccard-outliers-psi5.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-AE-Analysis-jaccard-outliers-psi3.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files'"
conda activate Fraserjaccard
cd $ABERRANTSPLICING
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-full-Analysis-jaccard-outliers.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-AE-full-Analysis-jaccard-outliers.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files'"
## Case Study
conda activate saseRPaper
cd $BASEDIR
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-threshold-Junctions-genes-full-analysis-Kremer-disease.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-Junctions-genes-full-analysis-Kremer-disease.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-threshold-jaccard-analysis-Kremer-disease.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-jaccard-analysis-Kremer-disease.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-full-Analysis-Kremer-disease.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-AE-Analysis-Kremer-disease.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
conda activate Fraserjaccard
cd $ABERRANTSPLICING
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-jaccard-full-Analysis-Kremer-disease.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/Fraser-PCA-Jaccard-AE-weighted-Analysis-Kremer-disease.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR'"
## Iterations
conda activate saseRPaper
cd $BASEDIR
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-0-iter-Bins-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-1-iter-Bins-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-3-iter-Bins-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-edgeR-Bins-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-0-iter-Junctions-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-1-iter-Junctions-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-3-iter-Junctions-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-edgeR-Junctions-full-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-0-iter-Junctions-genes-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-1-iter-Junctions-genes-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-3-iter-Junctions-genes-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
R --no-save --no-restore-data -e "rmarkdown::render('$ABERRANTSPLICING/fRUV-edgeR-Junctions-genes-analysis-Geuvadis.Rmd')" \
"--args output_directory='$ABERRANTSPLICING/Output_files' data_directory='$DATADIR' function_directory='$FUNCTIONDIR'"
# Figures
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Figure-Introduction.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$BASEDIR/Differential-usage/Figures/figures_paper.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Figure-GTEx-results.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTEXPRESSION/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Figure-Aberrant-splicing.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTSPLICING/Output_files' annotation_directory='$DATADIR/Geuvadis/Annotation' geuvadis_directory='$GEUVADIS'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Aberrant-expression-known-covariates.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTEXPRESSION/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Aberrant-expression-Scalability.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTEXPRESSION/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Convergence-filter.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTSPLICING/Output_files' annotation_directory='$DATADIR/Geuvadis/Annotation' geuvadis_directory='$GEUVADIS'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Kremer-Aberrant-expression.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTEXPRESSION/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Geuvadis-filtered-outliers-added.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTSPLICING/Output_files' annotation_directory='$DATADIR/Geuvadis/Annotation' geuvadis_directory='$GEUVADIS'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Geuvadis-hyperparameters.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTSPLICING/Output_files' annotation_directory='$DATADIR/Geuvadis/Annotation' geuvadis_directory='$GEUVADIS'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Geuvadis-intersection.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTSPLICING/Output_files' annotation_directory='$DATADIR/Geuvadis/Annotation' geuvadis_directory='$GEUVADIS'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Iterations.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTSPLICING/Output_files' annotation_directory='$DATADIR/Geuvadis/Annotation' geuvadis_directory='$GEUVADIS'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Figures-Kremer-jaccard-outliers-filtered-outliers-added.Rmd')" \
"--args output_directory='$FIGURESDIR/Output_files' data_directory='$ABERRANTSPLICING/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Table-1-Kremer-disease-genes.Rmd')" \
"--args data_directory_1='$ABERRANTEXPRESSION/Output_files' data_directory_2='$ABERRANTSPLICING/Output_files'"
R --no-save --no-restore-data -e "rmarkdown::render('$FIGURESDIR/Supplementary-Table-Kremer-disease-genes.Rmd')" \
"--args data_directory_1='$ABERRANTEXPRESSION/Output_files' data_directory_2='$ABERRANTSPLICING/Output_files'"