Genomic profiling of collaborative cross founder mouse strains infected with respiratory viruses to discover novel transcripts and infection-related strain-specific gene and isoform expression
RNA-Seq mRNA differential
Organism:
Mus musculus
Publication
- Xiong H, Morrison J, Ferris MT, Gralinski LE, Whitmore AC et al. (2014) Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.
Analysis Methods
Pipeline version | iRAP 1.0.1 |
Analyzed Libraries | |
Filtering Step 1 | Discard reads below minimum quality threshold |
Filtering Step 2 | Check of bacterial contamination; discard offending reads |
Filtering Step 3 | Discard reads with common uncalled characters (e.g. N) |
Filtering Step 4 | Remove reads from pair-end libraries that were orphaned by filtering steps 1-3 |
Read Mapping | Against genome reference (Ensembl release: 97) HISAT2 version: 2.1.0 |
Quantification | FeatureCounts version: 1.6.2 |
Differential Expression | DESeq2 version: 1.10.1 |
Gene Set Overlap | Fisher (non-directional), FDR < 0.1 using piano version |
Resources
