Input material | Unbiased random transcript fragments (hom. coverage) | Coverage bias (inhom. coverage) | Variable transcript start + poly-A (mod. TSS + polyA) |
---|---|---|---|
Alignment | Global; Transcriptome + Genome [tophat] | Local; Transcriptome + Genome [STAR] | Global; Transcriptome only [RSEM] |
Abundance | Read count (include multi-reads) [GenomicRanges: countOverlaps] | Read count(ignore multi-reads [HTSeq] | Isoform abundance model (resolve multi-reads [RSEM] |
Differential expression | Significance using a negative binomial count model [edgeR:exactTest] | Log-ratio effect size | |
Isoform switching | Differential isoform fractions [cuffdiff] | Differential splicing modules [DiffSplice] | Differential exons [DEXSeq] |