Links
Recommended Reading
- Recommended Coverage and Read Depth
- Illumina Coverage Calculator
- RNA-seq data analysis: Best Practices
- Aligner Comparison
- Guide to Analysis of RNA-seq Data
- Alignment Visualization software
- SeqAnswers
- Mothur (Microbial ecology)
- NEB rRNA Depletion
- Ribo-off rRNA Depletion (bacteria)
- riboPOOL
- Ribo Minus
- Gene Fusion Detection
- Alignment algorithms
DNA Analysis
- Franklin (variant classification)
- AmpliCancer - variant discovery tool
- SNPnexus
- Genome Analysis Tool Kit (GATK)
- Gemini (variant annotation)
- VarAFT
- Mutation Taster
miRNA Analysis
circRNA Analysis
ChIP-seq Analysis
Single Cell Resources
- 10x Genomics Publications resource
- 10x Genomics Analysis guides
- How many cells
- Cite-seq
- SEURAT
- Tutorial: guidelines for annotating single-cell transcriptomic maps
