Table 1.
Capabilities of BAMScale and other publicly available tools
| Tool | ||||||
|---|---|---|---|---|---|---|
| BAMscale | IGVtools | bedtools | MACS (callpeak followed by bedgraph2bigwig (UCSC)** | MACS (pileup followed by bedgraph2bigwig (UCSC)** | deeptools | |
| Creating coverage tracks | ||||||
| ChIP-seq/ATAC-seq | X | X | X | * | X | |
| ChIP-seq/ATAC-seq (normalized) | X | X | X | |||
| Log2 coverage (replication timing) | X | X | ||||
| OK-seq (RFD calculation) | X | |||||
| RNA-seq | X | * | * | * | X | |
| RNA-seq (splice-aware) | X | |||||
| Stranded coverage | X | X | ||||
| Quantifying peaks | ||||||
| Raw read counts | x | x | ||||
| Normalized read counts | x | |||||
* Scaling factor cannot be specified
** BAM file has to be pre-filtered for alignment quality