SpliceHarmonization: a harmonized method for identifying RNA splicing events in therapeutics for splicing modulation

GitHub link: https://github.com/interactivereport/SpliceHarmonization

Data Release:

simulation_data: Demonstrates the processed splicing event simulation.

simulation_data├── bam (# all simulated bam files for splicing analysis)├── fasta│   ├── combined_alt.fasta│   ├── combined_ref.fasta│   └── true_event_df.csv (# true simulated splicing event)├── simulation_num_{counts}_{alternative2control ratio}

SMN2_public_dataset: Contains all splicing analyses for one SMN2 public dataset (SRP334251), including rMATS, LeafCutter, MAJIQ, and SpliceHarmonization.

SMN2_public_dataset├── Original_res│   ├── bam  # (bam files removed due to size limitation, happy to disuccss!)│   ├── leafcutter│   ├── majiq│   ├── rmats│   └── stringtie└── SpliceHarmonization_res    └── {Comparison}        ├── harm        ├── harm_run_1.e.log        ├── harm_run_1.o.log        ├── harm_run_2.e.log        ├── harm_run_2.o.log        ├── harm_run_3.e.log        ├── harm_run_3.o.log        ├── harm_run_4.e.log        ├── harm_run_4.o.log        ├── junction_prep        ├── out        │   ├── all_cleaned.csv        │   ├── all_gene        │   │   ├── {gene_names}.csv (# events output for each gene)        │   └── mxe        ├── run1.sh        ├── run2.sh        ├── run3.sh        └── run4.sh

simulation_validation: Contains all splicing analyses for a simulation dataset, including rMATS, LeafCutter, MAJIQ, and SpliceHarmonization.

simulation_validation├── Original_res│   ├── leafcutter│   ├── majiq│   ├── rmats│   └── stringtie└── SpliceHarmonization_res    ├── {Comparison}    │   ├── harm    │   ├── harm_run_1.e.log    │   ├── harm_run_1.o.log    │   ├── harm_run_2.e.log    │   ├── harm_run_2.o.log    │   ├── harm_run_3.e.log    │   ├── harm_run_3.o.log    │   ├── harm_run_4.e.log    │   ├── harm_run_4.o.log    │   ├── junction_prep    │   ├── out    │   │   ├── all_cleaned.csv    │   │   ├── all_gene    │   │   │   ├── {gene_names}.csv (# events output for each gene)    │   │   ├── introns.csv    │   │   └── mxe    └── FinalMetric.csv (# summary evaluation information)

Files/folders in bold are final outputs