dphansti edited this page Apr 16, 2016 · 20 revisions

What does Mango do?

Mango processes ChIA-PET sequencing data (in fastq format) and determines statistically significant DNA-DNA interactions (loops) between pairs of genomic loci bound by the target protein. Mango performs the following five steps which can run all at once or one at a time:

  • Linker parsing: finds and removes linker sequences.
  • Read alignment: aligns reads to the genome using bowtie.
  • PET filtering: removes reads potential due to PCR duplication and organizes reads into bedpe format.
  • Peak calling: calls DNA binding peaks using MACS2.
  • Interaction calling: expceted interaction frequecnies are modeled based-on both peak depths and distances between peaks and statistically significant deviations are reported as interactions.

A detailed description of this steps can be found here.

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