GitHub - sivkri/splicing-events-calculation: Calculate five major splicing events using rMATS followed by annotation

splicing-variant-from-RNA-seq-data

Splicing_variant_calculation.sh - Calculate the splicing variants using rMATS turbo algorithm
Prepare the denovo GTF file by aligning Fastqc files with STAR aligner, followed by assemble using cufflinks
Merge_GTFs_from_de_novo_transcriptome - Merge the GTF file based on the class codes of cufflinks (optional step)
WT_Transcript_lengthscaledTPM - Prepare lengthscaled TPM values followed by counting through groups
WT_Splicing_Annotation - annotate the genes using ENSEMBL as reference with TPM value more than 0.6

Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
Merge_GTFs_from_de_novo_transcriptome.ipynb		Merge_GTFs_from_de_novo_transcriptome.ipynb
README.md		README.md
Splicing_variant_calculation.sh		Splicing_variant_calculation.sh
WT_Splicing_Annotation.ipynb		WT_Splicing_Annotation.ipynb
WT_Transcript_lengthscaledTPM.ipynb		WT_Transcript_lengthscaledTPM.ipynb
tpm_inclusion.R		tpm_inclusion.R