Table 1. Comparing solutions for ChIA-PET data analysis.
Linker trimming | Fuzzy search | Read alignment | PETs detection | PCR removing | Peak calling | Loop detection | Significant loop calling | Quality control | Allele-specific | |
---|---|---|---|---|---|---|---|---|---|---|
CPT | Half-linker | batman | Y | Y | Y | Y | Y | |||
ChiaSig | Y | |||||||||
MICC | Y | |||||||||
Mango | Half-linker | bowtie2 | Y | Y | Y | Y | Y | |||
ChIA-PET2 | Half-linker, Bridge linker | Y | bwa | Y | Y | Y | Y | Y | Y | Y |
The blank means the function is not supported by the tool. CPT and Mango is only capable for half-linker ChIA-PET data. ChiaSig and MICC only perform the significant loop calling step. When searching linkers, CPT and Mango use exact search while ChIA-PET2 can apply fuzzy search. Only ChIA-PET2 offers allele-specific analysis and quality control of ChIA-PET data.