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Table 1 Capabilities of BAMScale and other publicly available tools

From: BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks

 BAMscaleIGVtoolsbedtoolsMACS (callpeak followed by bedgraph2bigwig (UCSC)**MACS (pileup followed by bedgraph2bigwig (UCSC)**deeptools
Creating coverage tracks
 ChIP-seq/ATAC-seqXX X*X
 ChIP-seq/ATAC-seq (normalized)X  X X
 Log2 coverage (replication timing)X    X
 OK-seq (RFD calculation)X     
 RNA-seqX* **X
 RNA-seq (splice-aware)X     
 Stranded coverageX    X
Quantifying peaks
 Raw read countsx x   
 Normalized read countsx     
  1. * Scaling factor cannot be specified
  2. ** BAM file has to be pre-filtered for alignment quality