├── .gitignore ├── Alternative_Splicing ├── AS_Events.R ├── AS_Events_Output.R └── AS_Events_Output_novelannotated.R ├── Disease └── Disease.R ├── IsoSeq_Processing ├── Human │ ├── All_Batch_Processing_NewChem.sh │ ├── All_Batch_Processing_OldChem.sh │ ├── All_Demultiplex_Final.sh │ ├── All_FetalDemultiplex_Final.sh │ ├── All_Human_Demultiplex.csv │ ├── All_Human_Functions.sh │ ├── All_Human_Rarefaction.sh │ ├── All_Human_RawData_NewChem.txt │ └── All_Human_RawData_OldChem.txt └── Mouse │ ├── All_Batch_Processing.sh │ ├── All_Tg4510_Demultiplex.csv │ ├── All_Tg4510_Final.sh │ ├── All_Tg4510_Functions.sh │ ├── All_Tg4510_Rarefaction.sh │ └── All_Tg4510_RawData.txt ├── Novel_Genes ├── Antisense.R ├── Antisense_Novel_Genes.sh ├── Characterising_Novel_Genes.sh ├── Create_Novel_Genes_Antisense_Classification.R └── Create_Novel_Genes_Classification.R ├── Output ├── Correlations │ ├── Human_exon_length_isoform_correlation.txt │ ├── Mann_Whitney_LncRNA.txt │ ├── Mann_Whitney_NMD.txt │ ├── Mann_Whitney_Transcript_Exons_Novel_Transcripts.txt │ ├── Mann_Whitney_Transcript_Expression_Novel_Transcripts.txt.txt │ ├── Mann_Whitney_Transcript_Expression_Novel_genes │ ├── Mann_Whitney_Transcript_Length_Novel_Genes.txt │ ├── Mann_Whitney_Transcript_Length_Novel_Transcripts.txt │ └── Mouse_exon_length_isoform_correlation.txt ├── Figures │ ├── All_Plots.R │ └── All_Plots_Functions.R ├── Input_Variables.R ├── LongReadSequencing.Rmd ├── LongReadSequencing_Functions.R ├── Rmarkdowns │ ├── Alternative_Splicing.Rmd │ ├── Descriptive_Stats.Rmd │ ├── Fusion_Genes_All.Rmd │ ├── Human_Mouse_Comparison.Rmd │ └── Validation_Unnannotated_Genes.Rmd ├── SQANTI_General.R └── Tables │ ├── AS_IR │ ├── ALL_SUPPA2_Genes_Output_Updated.csv │ ├── ALL_SUPPA2_Genes_Output_Updated2.csv │ ├── Adult_IR_genes_only_IR_Transcripts.csv │ ├── Adult_Only_AS.txt │ ├── Fetal_IR_genes_only_IR_Transcripts.csv │ ├── Fetal_Only_AS.txt │ ├── Human_IR_genes_only_IR_Transcripts.csv │ ├── IR_gene_expression_Fetal_Adult.csv │ ├── Intron_Retention.csv │ ├── Mouse_AS_KnownGenes.csv │ ├── Mouse_AS_NovelAnnoIsoforms.csv │ ├── Mouse_IR_genes_only_IR_Transcripts.csv │ ├── SUPPA2_NumEvents_PerGene.csv │ ├── SUPPA2_Sum_No_Events.csv │ └── SUPPA2_Sum_No_Genes.csv │ ├── Adult_Only_AS.txt │ ├── All_Tables.R │ ├── All_Tables_Functions.R │ ├── Fetal_Only_AS.txt │ ├── GO │ ├── Adult_500topGenes.csv │ ├── Fetal_500topGenes.csv │ ├── Human_500topGenes.csv │ ├── Human_GOgwascata_100topGenes.csv │ ├── Human_GOmolecularfunction_100topGenes.csv │ ├── Human_IRGenes.csv │ ├── Mouse_500topGenes.csv │ ├── Mouse_GOgwascata_100topGenes.csv │ ├── Mouse_GOmolecularfunction_100topGenes.csv │ └── Mouse_IRGenes.csv │ ├── Human_Mouse_Comparisons │ ├── adult_fetal_all_NUM.csv │ ├── adult_fetal_all_NUM_fullymatched.csv │ ├── adult_fetal_multiexonic_NUM.csv │ ├── adult_fetal_multiexonic_NUM_fullymatched.csv │ ├── adult_fetal_multiexonic_TPM.csv │ ├── adult_fetal_multiexonic_TPM_fullymatched.csv │ ├── human_mouse_FSM_NUM_fullymatched.csv │ ├── human_mouse_all_NUM.csv │ ├── human_mouse_all_NUM_homology.csv │ ├── human_mouse_multiexonic_NUM.csv │ ├── human_mouse_multiexonic_NUM_fullymatched.csv │ ├── human_mouse_multiexonic_NUM_homology.csv │ ├── human_mouse_multiexonic_NUM_homology_fullymatched.csv │ ├── human_mouse_multiexonic_TPM.csv │ ├── human_mouse_multiexonic_TPM_fullymatched.csv │ ├── human_mouse_multiexonic_TPM_homologs.csv │ └── human_mouse_multiexonic_TPM_homologs_fullymatched.csv │ └── IR_gene_expression_Fetal_Adult.csv ├── Pipeline_Optimisation ├── CCS_ERCC_Parameters │ ├── IsoSeq_Testing.Rmd │ ├── IsoSeq_Testing.html │ ├── Testing_CCS_Parameters_Part1.sh │ ├── Testing_CCS_Parameters_Part2a.sh │ └── Testing_CCS_Parameters_Part2b.sh ├── CupcakeCollapse.Rmd ├── CupcakeCollapse.html ├── ERCC.Rmd ├── ERCC.html └── ERCC │ ├── 1_align_runtama.sh │ ├── 2_pipeline_comparison.Rmd │ ├── 2_pipeline_comparison.html │ └── ERCC.config ├── README.md ├── RNAseqvsISOseq └── RNASeqvsIsoSeq_Expression.R ├── Utilities ├── Disease_Genes │ ├── FinalDiseaseList.csv │ ├── SFARI-Gene_genes_07-29-2020release_08-07-2020export.csv │ ├── SZ_CLOZUK_GENE.txt │ └── SZ_PGC2.txt ├── Images │ ├── AS_Events.png │ └── bioinformatics_pipeline.png ├── Web_Resources │ ├── ColourAnnotateBed12.R │ └── Hub_processing.sh └── primer.fasta └── Whole_Transcriptome_Paper.Rproj /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SziKayLeung/Whole_Transcriptome_Paper/HEAD/.gitignore -------------------------------------------------------------------------------- /Alternative_Splicing/AS_Events.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SziKayLeung/Whole_Transcriptome_Paper/HEAD/Alternative_Splicing/AS_Events.R -------------------------------------------------------------------------------- /Alternative_Splicing/AS_Events_Output.R: 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