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Is it better to apply for Engineering Physics (in COE) or General physics (in CLS) at Berkeley?
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Essentially, I have a slightly weak application in terms of AP/Honors coursework so I am leaning against applying to the COE, but I want to know whether that should deter me.

cal
UCBerkeley

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What do you want to do with what you study? Berkeley is difficult to get into no matter what—the difference in difficulty between COE and CLS really will not be as significant as it might feel, and their academic thresholds in particular will be largely the same (i.e., if you're just worried about a lack of AP courses, applying to CLS vs. COE shouldn't make much of a difference). You should apply to the one that a) better fits your goals for the future and b) better fits what your profile. If you want to be an engineer and have the career opportunities associated with that—basically, if you want to build things, design things, work for engineering firms, etc., you should apply to COE and aim to study Engineering Physics. If you're more interested in pure scientific research (either in industry with a B.S. or after further graduate school) or physics as a platform to more typical jobs, go for General Physics. Even though they seem similar, there is a real difference between what each curriculum will set up for you, and that should imo be your biggest consideration when you aim for one.

(Incidentally, Berkeley is set up in a way that makes transferring between "impacted majors," of which all of their engineering majors typically are. So if you want to become an engineer, applying into CLS and attempting to internal transfer may not ultimately work out, no matter how good you are, if all of their spots are taken.)

Can't I become an engineer with a pure physics degree? and then maybe grad school for EE/ME?
It's possible, but you would need to go outside the major and take undergraduate engineering courses to give yourself the necessary foundation in the subject. Pure physics won't cover all the same areas as engineering physics, so if you want to make the switch afterwards, you'd need to make up ground.
Pure physics is a pretty theoretical degree. It sets you up well to do research in physics, or go to graduate school in things like astrophysics, but it's not designed as a springboard into engineering. It also could limit your opportunities for engineering co-ops and internships, as depending on the school engineering students might get priority. Bottom line, if your goal is to become an engineer, I would aim to study engineering unless there's a very good, non-admissions reason why not to.
i have strong interest in particle physics... engineering is moreso back up than anything.
Then by all means go for pure physics! The general point is that you should apply for the thing that's closer to what you want to study, and if that's particle physics, then pure physics would be the way to go. You'd be working with professors who specialize in that kind of thing, and would likely have research opportunities that engineers might not have access to.
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What do your ECs look like? How easy is it to transfer in and out of each major? I think you should consider that before choosing.

I am doing indy research which i enter into the science fair every year (some awards), science Olympiad, academic decathlon (where I am co president of team) and music stuff. It is hard to transfer from CLS to COE but not vice versa