https://github.com/sivkri/splicing-events-calculation
Calculate five major splicing events using rMATS followed by annotation
https://github.com/sivkri/splicing-events-calculation
splicing splicing-analyses splicing-annotation splicing-detection splicing-event splicing-event-filter splicing-quantification splicing-visualization
Last synced: 10 months ago
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Calculate five major splicing events using rMATS followed by annotation
- Host: GitHub
- URL: https://github.com/sivkri/splicing-events-calculation
- Owner: sivkri
- Created: 2021-11-05T12:06:36.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2021-11-05T12:48:13.000Z (over 4 years ago)
- Last Synced: 2025-03-22T19:37:34.860Z (about 1 year ago)
- Topics: splicing, splicing-analyses, splicing-annotation, splicing-detection, splicing-event, splicing-event-filter, splicing-quantification, splicing-visualization
- Language: Jupyter Notebook
- Homepage:
- Size: 25.4 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
## splicing-variant-from-RNA-seq-data
1. Splicing_variant_calculation.sh - Calculate the splicing variants using rMATS turbo algorithm
2. Prepare the denovo GTF file by aligning Fastqc files with STAR aligner, followed by assemble using cufflinks
3. Merge_GTFs_from_de_novo_transcriptome - Merge the GTF file based on the class codes of cufflinks (optional step)
4. WT_Transcript_lengthscaledTPM - Prepare lengthscaled TPM values followed by counting through groups
5. WT_Splicing_Annotation - annotate the genes using ENSEMBL as reference with TPM value more than 0.6