Chip-exo peak-pair distribution heatmap

Question

[sourav.por]

Hi,

Recently I am working with ChIP-exo data and I seperate out maped Chip-exo reads in two files, forwerd and reverse strand.

I have tried the ngsplot for generating a heatmap of peak-pair distribution of mapped reads, but could not able to get desired output.

Can anyone helpme out to make the peak-pair distribution heatmap from forward and reverse strand mapped reads.

Answer 1

[dnaseiseq]

For CHIP-EXO, CexoR: An R/Bioconductor package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Answer 2

[Ming Tommy Tang]

you may use MACS for ChIP-exo https://github.com/taoliu/MACS/issues/15

Answer 3

[Tulip Nandu]

You can also use HOMER to generate the heatmaps. They can tell you the gained, maintained and lost peaks between the conditions.