Combining the ChIP-Seq Data

[ayushraman]

Hi everyone,

I am interested to know if I am allowed to combine the Chip-Seq data from experiments where the sample was same (under same conditions i.e. two replicates) but was ran on different machine where one was run on Illumina GAII and other was run on the Illumina Hi-Seq ? Also could you please provide me some source or journal publications where the scientists might have used the similar approach ?

Thanks.

[Simon Anders]

This depends a lot on what you intend to do with your reads once you have combined them.