From Geuvadis MediaWiki
Description of data analysis: methods and results.
- mapping of mRNA data, comparison results
- mRNA Quantification
- Exon, transcript, slice junction, n-TAR etc quantifications
- sample and sequencing quality assessment, normalization and covariates, batch effects
- Sandbox dataset for testing
- information of the sandbox datasets of 5 and 24 samples for methods/QC testing purposes
- Genetic variation data
- Which genetic data will be used, imputation methods, filters, formats, variant annotation
- A2 Variant Calling
- Variant calling from RNAseq, DNA-RNA differences
- A3 mRNA Variation
- Allele specific expression
- Methods and results of ASE analysis
- Allele specific alternative splicing
- Methods and results of ASAS analysis
- Transcriptome QTLs
- Various QTL analyses
- Normalization of transcriptome phenotype quantifications
- Basic miRNA analyses
- phred scores, clipped reads, mappings, quantification etc.
- Differential Expression
- gene differential expression based on read counts
- Percentage Splicing Index
- Measuring Exon Inclusion Levels
- Ubiquity vs specificity of gene and isoform expression across populations
- Consistency of gene and isoform expression within and between populations
- Differential isoform usage
- For which genes do we observe differences in the relative abundances of their isoforms across populations?
- miRNA-mRNA interaction
- How does miRNA expression regulate mRNA levels?