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PLEASE help me decide on an admissions decision!! Or advice MS programs microbiology/immunology

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I had applied to PhD programs last December for Fall 2020 Admission- sadly I was rejected from all the programs I applied too. I have working in microbiology R&D research for about two years now (in June) I thought this was enough research experience for a PhD. I know my end goal is a PhD and thought I had participated in enough research, researched the jobs I want (which require a PhD), talked to professors in the field to see if I am ready for a PhD or if it is necessary, and understand the commitments needed for a PhD etc. etc. This is why I applied for next fall admissions. From the feedback from the schools I was rejected from, it seems my industry research isn't valued and I need academic research experience. Therefore, when I was rejected I had options of quitting my (high paying) job for academic research experience, volunteering in lab, finding other ways to improve my application or apply to MS programs. 

Fortunately, New York Medical College has accepted me for their MS program in Microbiology and Immunology for Fall 2020 admissions. This department research aligns with my research goals and they have a research thesis that I can gain the academic lab experience that I am lacking. Also, I can stay at my current job for the first year while taking classes (my boss is flexible with my hours) while my company provides tuition reimbursement. Once, I start the research thesis I would probably need to quit my current job. Therefore, by the time I need to start my research thesis after class work I can save up enough money to pay for the rest of the program and not take out loans. This was a huge plus for me because I can continue my current research, start a masters program, and in the long run apply again to PhD program with a stronger application and more direction of my research goals. A problem is this program isn't as well known or isn't as strong as I would like- but thinking it is just for a masters degree it might not matter the strength, the research I do is probably more important!! Additionally, there is an option to work at the lab you are doing research at. The class times of this program also 

But, recently I was accepted to University of Rochester Microbiology MS program (fall 2020) with 30% tuition coverage. The program, with this scholarship, is still expensive and I would probably have to take out loans to cover the cost of living and tuition for two years. But, this program's department research aligns with my research goals and also has an intensive research experience. I loved the program's goals when I had an interview as well. Also, University of Rochester is more well known. I would also need to quit my current job, which makes me nervous because I have a job while there is a recession due to COVID. 

If I decide to do a PhD at the program I am getting a masters at University of Rochester seems better than NYMC. But, if I end up deciding to change institutions for a PhD or decide to go to another school (depending if I get accepted) then NYMC seems better since I will come out of the program with no loans. I already have significant loans from undergrad so this is a huge factor in the decision - I have been putting a large chunk of my paycheck to pay them off but I still have a lot left. 

If I end up doing ONLY and MS program do you think, job wise, they will put significance on which program is stronger? 

Which would you do, a program that makes more sense financially or a program that has stronger or more well known research? 

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