I wonder there are several programs for analyzing chip seq data and mostly it is algorithm for peak detection which is different. Some of available programs include- Seqmonk, Partek, R etc etc. My question is if we do analysis is in one it will have one list of regions and follow second it will be different so what will be the easiest rule to follow one. More less this was the same issue when expression arrays were started. Any suggestion will be highly appreciated. It look like one person will like one program while other may prefer second and so on.![Cool](https://www.seqanswers.com/core/images/smilies/cool.png)
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