The provided Snakemake workflow and source code reproduce the PSI plots for alternative splicing events in a murine heart failure model and human engineered heart tissue.
Therapeutic inhibition of RBM20 improves diastolic function in preclinical models of heart failure.
# Source code to produce the PSI plots The scripts were used to generate the PSI plots to appear in Radke, M and Badillo-Lisakowski, V et al "Therapeutic inhibition of RBM20 improves diastolic function in a murine heart failure model and human engineered heart tissue". deposited for reproducibility purposes. The workflow is based on Snakemake, see `Snakefile` for more information. Workflow was called with ```bash snakemake --configfile config. yml --printshellcmds --cluster "sbatch --mem cluster. mem --out cluster. out --error cluster. out -c cluster. c --parsable " --cluster-config cluster. yaml --jobs 10 ``` ## Dependencies: - stringtie/1. 3. 5 - cufflinks/2. 2. 1 - python2 - R/3. 5. 1 - perl - bedtools Dependencies were handled with Environment Modules. ## Workflow steps: 1. Guided transcriptome assembly with StringTie: - Parameters: - minᵢsoformfraction: 0. 2 - minₐnchorₗength: 8 - minⱼunctioncoverage: 3 - reference: /biodb/genomes/musₘusculus/GRCm38₈5/GRCm38. 85. gtf The modified GRCm38 84 annotation accopanies this repository. The version of Ensembl has been used to study Titin and match the exons to domains. 2. Merge annotation with cuffmerge: - Parameters: - reference: /biodb/genomes/musₘusculus/GRCm38₈5/GRCm38. 85. gtf - minᵢsoformfraction: 0. 2 3. Find 'containers', loci with that contains alternative splicing events, and calculate PSI from STAR `SJ. out. tab` intron counts with computePSI. pl PSI is define by the ratio between the number of reads including an exon and total reads for that event (reads including + reads excluding). 4. Produce the plots using PSIₚlotₐso. R script: One plot per gene, only for gene with two or more exons, in addiiton: - Removde duplicated exons - Merged overlapping exons The accompanying test data reproduces figure 4. b of the paper: `Rscript testdata/PSIₚlotₐso. R testdata/output/ testdata/ldb3. gtf testdata/` The subset of the data was prepared with: ```fish set gtf "/beegfs/prj/MitchGotthardt/Thiago/psiₚlots/Musₘusculus. GRCm38. 84cleaned. gtf" grep 'geneₙame "Ldb3";' gtf | sort -k1, 1 -k4, 4n | bedtools merge -d 1000000 -s -c 5, 6, 7 -o first > testdata/ldb3. bed intersectBed -b testdata/ldb3. bed -a gtf -wa -s > testdata/ldb3. gtf for f in stringtieguided/*/psi. txt; mkdir testdata/ (basename (dirname f) ) ; intersectBed -b testdata/ldb3. bed -a f -wa -s > testdata/ (basename (dirname f) ) /psi. txt; end ```
Thiago Britto‐Borges (Fri,) conducted a other in Heart failure. RBM20 inhibition was evaluated. The provided Snakemake workflow and source code reproduce the PSI plots for alternative splicing events in a murine heart failure model and human engineered heart tissue.