Feeling Huge Pressure from Cost of Sequencing and Limited Knowledge

[breadwinner]

I have been in my lab for almost one year. I have extracted some challenging RNA samples from a few non-model organisms. I have already sunk money (my advisor's) into my work due to needing kits and reagents, not to mention a year of stipend. Now that it comes time to sequence my samples I am feeling completely overwhelmed by the costs (which in my mind equate to pressure on me for the payoff to be excellent) plus the fact that due to my semi-inexperience with buying sequencing services I keep getting the price wrong, thinking it's lower than it really is, having my advisor sign a PO after convincing him it's worth it, only to discover new hidden fees that add hundreds or thousands of dollars. Meanwhile, one of my samples is slightly impure compared to the others but after redoing it over and over the quality only gets worse, do we could be gambling at least in part on a low quality sample.  

I feel that if I convince my advisor to gamble thousands of dollars on my work I'm just setting myself up for failure if the results of sequencing are less than perfect. Every time the price increases I feel very upset at having to go through the cycle of asking for money again because I feel like it's my fault the price is so high. I've tried hard to get the price right but because I am still learning what all the Illumina terms mean it's very challenging to know even after talking to tech support. 

I didn't realize when I designed this experiment that it would cost so much because my other professor (who has more sequencing experience) kept telling me it would be super inexpensive. I can't tell if my emotions make no sense and I should just force myself to ask for the huge amount of money needed for the appropriate specs or if I should be working on somehow making it cheaper. The latter is something I have no idea how to do. Pls help. Is any of this normal? I know I've screwed up majorly getting the price wrong but I really thought I had it right every time...

[TakeruK]

I am not in your field nor your lab so I can't say for sure, but you might also be overthinking this. Science costs money and your PI is prepared to spend that money. You should not blame yourself for spending your PI's money. And you should definitely not feel bad that you are costing your PI the amount of your stipend! You did the work and accomplished challenges. You deserve to be paid for your work, whether or not it results in a payoff. Your work has value on its own right.

From your post, it's not clear if your pricing mistake is something that your PI was actually upset with you or if you are imposing this stress onto yourself. If you have not had a discussion with your PI about this incident, you should definitely do so. Apologize for your mistake, explain that you have learned the cause of that error and don't be afraid to ask more questions in the future about ordering materials. If your PI is too busy to help you on this directly, ask if they can point you to a resource to ensure you understand how ordering materials work (e.g. a senior grad student, a postdoc, a lab manager, admin assistant etc.) From this conversation, you can probably figure out if this was a big deal or if it was nothing. A lot of terms are subjective, e.g. do you know the actual dollar amount the the other prof had in mind when they said it was "super inexpensive"? For some research groups, this could mean tens of dollars, while for others, super inexpensive could mean thousands of dollars.

Finally, for your current sample, you should talk to your PI about the quality. Before you come into this conversation, it could be helpful to figure out how much better the results would be if you had the purer sample, and then let the PI decide whether they want to spend the money for the increased in data quality. If you don't know how to do this, then come to the conversation by presenting the facts and asking your PI for input on how you could determine how much impact the impurity has on your intended results. It could help if you had come up with some ideas yourself (even if you are not sure they would work).

[hats]

Can you talk to other graduate students in your program about their costs? As far as I understand it, science is expensive! Surely at least one other student—especially the students closer to graduating—has had this happen and can commiserate and advise. You will probably get good advice here, but I bet it will make you feel less alone if you know someone in your actual program has gone through this, too.

There's also evidence within your post that costs for this kind of thing can be widely variable and figuring them out is difficult, and that they aren't something everybody always gets right immediately or every time. After all, your other professor, who's been doing this for much longer than you have, got your costs extremely wrong.

[breadwinner]

Thanks guys  

1 hour ago, TakeruK said:

From your post, it's not clear if your pricing mistake is something that your PI was actually upset with you or if you are imposing this stress onto yourself.

TakeruK, I have trouble making this distinction myself. I am pretty sure based on past experiences that I am imposing at least 80% of it on myself. My advisor is kind and soft-spoken but I am always paranoid that something that I've done will be the last straw, because it seems to me that I am making a lot of egregious mistakes. His response was pretty neutral. Obviously he would have liked me to get it right the first time but he didn't criticize me at all for getting it wrong and said my apology was unecessary. 

I think one of my prroblems is that none of the students in my lab have sequenced before. The last one to do this graduated before I came here. 

Anyway, I will try to overcome my qualms and push forward. 

[TakeruK]

1 hour ago, breadwinner said:

Thanks guys  

TakeruK, I have trouble making this distinction myself. I am pretty sure based on past experiences that I am imposing at least 80% of it on myself. My advisor is kind and soft-spoken but I am always paranoid that something that I've done will be the last straw, because it seems to me that I am making a lot of egregious mistakes. His response was pretty neutral. Obviously he would have liked me to get it right the first time but he didn't criticize me at all for getting it wrong and said my apology was unecessary.

That sounds like a good reaction, to me, not just "neutral"! I think we just need to take what our advisors say at face value and stop trying to overinterpret their reactions. Everyone makes mistakes and I think everything is fine.

If it makes you feel better, someone in my group once booked a flight to the wrong city for a work trip once! There was a small cost to change the reservation (few hundred dollars) but that was small compared to the total cost of the trip/work. And I have booked a flight home on the wrong day once (it was a red-eye and I misread the leaving/arriving dates). I wanted to leave late on the final day of the conference but I accidentally booked it for a late flight on the day following the final day! Everyone overlooked it because no one expects you to leave hours after the last talk ended, it's more standard to leave the next morning/afternoon instead. So, the change fee for the flight was an extra charge, but on the bright side, that fee was smaller than the cost of an extra night stay so the grant paid for it.

1 hour ago, breadwinner said:

Anyway, I will try to overcome my qualms and push forward. 

Sounds good---just wanted to say though that if you are not sure if the samples you have now are pure enough, it might be a good idea to discuss this with your advisor to figure out if the work you're about to do on these impure samples will yield satisfactory results. Generally, it might be worth a few checks so that you don't sink more time/effort/money into a sample that won't be good enough.

[samman1994]

This is something I've personally done, and really depends on the professor and your relationship with them, and what kind of people you both are. Personally, I like to become close to my professor, in regards to research and personally. As in, when things get tough and I need help, I go sit down and talk to them (when they have the time). I will set an appointment with them, and tell them my research concerns, and my emotions regarding said concerns. Most PIs want to see you succeed, and want to help you succeed. It sounds to me like your PI seems like a very understanding and nice person. That said, I'd just talk to him about the concerns. Tell him, I'm sorry I've kept getting prices or experiment set up wrong, sorry for wasting your money etc. Then I'd tell him emotionally how much it bothers me. Most likely, not only will your PI offer you some emotional help and tell you its fine, or normal and stuff like that happens all the time, but they can also offer you advice on where to go and how to fix the problem itself. 

I had a similar issue myself with an SPR that we bought for the sole purpose so I alone could test binding. I ended up wasting at least 10+ chips and multiple samples (I had never used SPR prior and my PI just said have fun go crazy). She ended up asking me one day why we were ordering so many chips and parts, and I told her because I messed up and didn't know how to use the SPR and basically proceeded with trial and error. I told her how bad I felt that I kept messing up and wasting money, and felt like I should have gotten it by now, etc. She told me SPR is difficult regardless, especially for me since I had no training was self teaching essentially, and ended up helping me out a bit to the point where I resolved the problem shortly after and got amazing results. Made me feel less like an idiot, and helped me with my problem too. 

Edited August 19, 2017 by samman1994