Acknowledgement
This project is funded by NSF award ABI-1661152.
- Home
- NGS Workflow Overview
- RNA-Seq Workflow
-
ChIP-Seq Workflow
- 1. Introduction
- 2. Workflow environment
- 3. Read preprocessing
- 4. Alignments
- 5. Utilities for coverage data
- 6. Peak calling with MACS2
- 7. Annotate peaks with genomic context
- 8. Count reads overlapping peaks
- 9. Differential binding analysis
- 10. GO term enrichment analysis
- 11. Motif analysis
- 12. Version Information
- 13. Funding
- 14. References
-
VAR-Seq Workflow
- 1. Introduction
- 2. Workflow environment
- 3. Read preprocessing
- 4. Alignments
- 5. Variant calling
- 6. Filter variants
- 7. Annotate filtered variants
- 8. Combine annotation results among samples
- 9. Summary statistics of variants
- 10. Venn diagram of variants
- 11. Plot variants programmatically
- 12. Version Information
- 13. Funding
- 14. References
-
RIBO-Seq Workflow
- 1. Introduction
- 2. Load workflow template
- 3. Read preprocessing
- 4. Alignments
- 5. Read distribution across genomic features
- 6. Adding custom features to workflow
- 7. Genomic read coverage along transripts or CDSs
- 8. Read quantification per annotation range
- 9. Analysis of differentially expressed genes with edgeR
- 10. GO term enrichment analysis of DEGs
- 11. Differential ribosome loading analysis (translational efficiency)
- 12. Clustering and heat maps
- 13. Render report in HTML and PDF format
- 14. Version Information
- 15. Funding
- 16. References
- Training Events
- Publications
- Acknowledgement
- Contacts