Page Index - Magdoll/cDNA_Cupcake GitHub Wiki
30 page(s) in this GitHub Wiki:
- Home
- What is cDNA_Cupcake
- How to use the scripts
- Installing Cupcake (optional)
- Basic Nucleotide Assumption
- Current list of maintained scripts
- Annotation and Rarefaction
- Targeted Iso-Seq Analysis
- Sequence Manipulation
- Cupcake ToFU: supporting scripts for Iso-Seq after clustering step
- List of Other Useful Tools
- Annotation and Rarefaction Wiki
- Best practice for fusion transcript finding
- Cupcake: supporting scripts for Iso Seq after clustering step
- Handling multiple samples: Creating a master transcriptome
- How to create a pigeon‐compatible annotation GTF
- Iso Seq Public Datasets
- Iso Seq Single Cell Analysis: Recommended Analysis Guidelines
- IsoPhase: Haplotyping using Iso Seq data
- MagPhase: Haplotyping using Iso Seq data for metagenomics samples
- Sequence Manipulation Wiki
- Targeted Iso Seq QC Wiki
- Tutorial: Analyzing MAS Seq data with popular community tools
- Tutorial: APIs for reading SAM, GFF, etc...
- Tutorial: Collapse redundant isoforms without genome
- Tutorial: Command Line Crash Course
- Tutorial: Demultiplexing SMRT Link Iso Seq Jobs
- Tutorial: Iso Seq Bioinfx hands on
- Tutorial: Troubleshooting SMRT Link MAS Seq Single cell Iso Seq output
- Tutorial: Working with PacBio's CCS BAM and SMRT Tools