Table 1.
Comparison of Manananggal to other visualization methods for alternative splicing events
| Manananggal | IGV | SpliceSeq | DEXSeq | |
|---|---|---|---|---|
| Input | BIGWIG + COUNT_FILE | BAM | fastq | BAM |
| Organism | Human/Mousea | All | All? | All |
| Interactive | ✓ | ✓ | ✓ | (✗) |
| Unexpressed isoforms can be hidden | ✓ | ✗ | ✗ | (✗) |
| Coverage plots are available to spot differential expression | ✓ | ✓ | ✗ | ✓ |
| Indication of overlapping antisense transcripts | ✓ | ✓ | ✗ | (✗) |
| gene/transcript structure | full | full | reduced | reduced |
| introns | compressed | to scale | compressed | to scale |
| Indicates AS exons | ✓ | ✗ | ✓ | ✓ |
| Allows group comparisons | ✓ | ✗ | ✓ | ✓ |
aIn principle Manananggal should also work with other organisms. Some functions, such as the cross-reference table are not available for other organisms and thus users would need to use gene IDs rather than symbols to query genes
The DEXSeq plot is an R function that could be modified to add some of the missing features