Table 1 Summary of available tools
CisGenome[17] | BEDTool[25] | HOMER[18] | Podbat[19] | Cistrome[20] | EpiExplorer[21] | GAT[22] | PscanChIP[23] | PAVIS[24] | ChIPseek | |
|---|---|---|---|---|---|---|---|---|---|---|
Web-based analysis tool | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
Graphic user interface | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |||
Annotation | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||
Plot of position relative to TSS | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
Plot of peak length distribution | ✓ | ✓ | ||||||||
Filter (by peak length) | ✓ | ✓ | ||||||||
Filter (by position relative to TSS) | ✓ | |||||||||
Post-filter analysis | ✓ | |||||||||
Motif identification | ✓ | ✓ | ✓ | ✓ | ✓ | |||||
Comparison | ✓ | ✓ | ✓ | ✓ | ✓+ | ✓ | ✓ | |||
Link to UCSC genome browser | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
Plot of genomic location | ✓ | ✓ | ✓ | ✓ | ✓ | |||||
Sequence extraction | ✓ | ✓ | ||||||||
Built-in peak databases | ✓ | ✓ | ✓ | |||||||
Enrichment analysis | ✓ | ✓ | ✓ | ✓ | ✓ |