Table 2 Examples of software packages for analyzing 5′-end data (including CAGE)
From: CAGEfightR: analysis of 5′-end data using R/Bioconductor
Tool | Implementation | Input data | Tag Clustering | TSS candidate shape | Differential Expression | Gene-level analysis | Unique features |
|---|---|---|---|---|---|---|---|
MOIRAI [29] | Graphical User Interface | FASTQ | paraclu [30] | None | None inbuilt | None | rRNAdust, TagDust [31] |
RECLU [32] | Bash | BED | modified paraclu [30] | None | edgeR [33] | None | Hierarchical TSSs |
CAGEr [34] | R/Bioconductor | BAM | distance or paraclu [30] | IQR | DESeq2 [35] | Gene expression | G-bias correction [36], power-law normalization, TSS shifts |
icetea [37] | R/Bioconductor | FASTQ | Sliding window | None | edgeR [33] | Gene expression | Paired-end methods, mapping via R |
TSRchitect [38] | R/Bioconductor | BAM | X-means | Shape Index [17] | None inbuilt | None | Paired-end methods |
CAGEfightR | R/Bioconductor | BigWig | Slice-reduce | IQR, entropy, etc. | None inbuilt | Gene expression and alternative TSS usage | Enhancer calling, TSS-enhancer co-expression, super enhancers |