Is it bad to take some courses at one JC and some at another JC for two years before transferring to a 4 year? ( one is a quarter system and the other is semester).
No problem. Hopefully your GPA at each was high. AMCAS will translate all grades into semester equivalents so they are directly comparable when you apply there.
As long as you don't appear to be skipping off to a JC every time a tough prereq comes along it's fine. The MCAT is the great equalizer anyway. The main problem with CC's and JC's is they're generally not as well-equipped for pre-professional students as 4-year universities in terms of opportunities for research, volunteering, extracurriculars, leadership etc. The quarter vs. semester systems play no part as far as I know.
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