Chip Seq which program to follow

[honey]

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.

[simonandrews]

It look like one person will like one program while other may prefer second and so on.

I think you hit the nail on the head right there.

I'm not saying that there aren't differences between different programs for the analysis of ChIP-Seq data but there isn't going to be a single answer to which is the 'best'.

You may find that some peak finding methods are more appropriate to certain kinds of ChIP-Seq than others (say transcription factors vs MeDIP vs histone mods) so the answer may partly depend on what type of data you have. You may also be influenced by your level of computer knowledge - using a command line linux app can be daunting if you've only ever used windows, and a graphical app may be a pain if you've got 100 samples to process.

You may also want to look at the level of flexibility you have available. Do you really just want to do peak detection, or might you want to look at just analysing all promoters (for example), again this might point you towards a different subset of programs.

The final thing to consider is if you know anyone who is comfortable using any of these systems already. Places like SeqAnswers are great, but there's nothing like having someone who already knows a package and who can come and help you out if you get stuck!