u/PrincipleDense5592

Basically just wanting some advice from other grad students who are going/have been through it.

I started grad school a few years back as a Master's student, and was kind of convinced by my PI to stay as a PhD student and I did a Masters to PhD transfer within the program, so I will no longer receive a Masters but hypothetically just the PhD. I am now in my third year of grad school, which is being considered year 3 of my PhD.

I have been miserable this entire time. I had a severe substance abuse issue for the first two years during my Master's and developed a significant amount of depression. I've been on medication for about 6 months now, 8 months sober, and the depression has just maintained or gotten worse. I am absolutely miserable, my funding has gotten cut from a pretty low amount to an even lower amount and I can't keep up with tuition and living expenses. In terms of career goals, I have absolutely zero desire to stay in research (for context I am in bioinformatics and cancer genomics), and have absolutely no passion or interest in my project. I want to get into business, consulting, or even patent work.

Considering the significant mental health toll and the financial burden with my career goals in mind, should I even continue or just master out? I have been applying to jobs and have had several interviews for sales jobs, which is much more attractive to me than staying in school.

Thanks in advance!

Basically just wanting some advice from other grad students who are going/have been through it.

I started grad school a few years back as a Master's student, and was kind of convinced by my PI to stay as a PhD student and I did a Masters to PhD transfer within the program, so I will no longer receive a Masters but hypothetically just the PhD. I am now in my third year of grad school, which is being considered year 3 of my PhD.

I have been miserable this entire time. I had a severe substance abuse issue for the first two years during my Master's and developed a significant amount of depression. I've been on medication for about 6 months now, 8 months sober, and the depression has just maintained or gotten worse. I am absolutely miserable, my funding has gotten cut from a pretty low amount to an even lower amount and I can't keep up with tuition and living expenses. In terms of career goals, I have absolutely zero desire to stay in research (for context I am in bioinformatics and cancer genomics). I want to get into business, consulting, or even patent work.

Considering the significant mental health toll and the financial burden with my career goals in mind, should I even continue or just master out? I have been applying to jobs and have had several interviews for sales jobs, which is much more attractive to me than staying in school.

Thanks in advance!

Hello,

Just curious if anyone has experience with their OSAP being recalculated and seeing a dramatic reduction in the amount?

For context I am a grad student in Faculty of Science at my institution and rely on OSAP to help with paying rent, living expenses etc as my stipend/TA funding only goes so far and I have not received any major scholarships. My OSAP was calculated back in June (all loans, no grants) and then suddenly yesterday, it was reduced to 1/10th of the loan amount to just a few hundred dollars to cover both the fall and winter term.

Was wondering if anyone else has experienced this? I plan to go to the financial aid office immediately on Monday but I'm just panicking a bit currently!

Thanks in advance

Hello,

I have a dataset of about 35 bulk tissue (healthy, adult age somatic tissue) samples each sequenced to 40X depth via PacBio HiFi sequencing, and have performed variant calling with 3 callers (DeepVariant, Pepper-Margin-Deepvariant, Clair3) for SNVs/indels, and about 7 callers for SVs.

My variant call data is seriously inflated with germline variants, talking hundreds of thousands of SNV calls for my samples which are inbred mice, so this number is a huge red flag. I have tried quality based filtering, removing any variant with VAF>0.30, QUAL<20, GQ<20, and DP<10 and >75. However, this still leaves me with thousands of variants.

I am at a loss on what to do to reduce this noise and to get at the actual mosaic variant signal. The goal here is to identify tissue-specific mosaic variants in each mouse, but I feel like I'm running in circles trying to properly reduce the noise and get at the expected amount for bulk tissue analysis at my depth, which appears to be 20-60 SNVs per tissue according to some brief searches.

Any suggestions? I wonder if its the tools I am using, or if its just the filtering criteria I am selecting.

Thanks in advance!