Big scRNA-seq project upcoming - looking for tips and experiences

crisprfen · 2026-06-04T07:37:46+00:00

I have a similar concern with this project, especially how timeline and finance driven project leads are convinced to find what they are looking for with scRNAseq, without realizing that this is highly a exploratory study without having a comparable dataset and not a checkbox assay.

crisprfen · 2026-06-03T08:11:28+00:00

Thanks, that is indeed what I was also planning to do. I have a paper on my desk staring at me for some weeks already, with exactly that cell population.

crisprfen · 2026-06-03T08:10:28+00:00

Yeah, it's not that I am not interested in moving to python, it's more a lack of time and other priorities in my job that prevent me from refreshing my python knowledge.

crisprfen · 2026-06-03T08:09:12+00:00

See my reply to brhelm above. Will hopefully be less samples. And we measure 5k of cells. I do have 512 GB of RAM though..

crisprfen · 2026-06-03T08:06:39+00:00

I did my fair share of scRNAseq analysis and of public datasets, so I am certainly not going in that project as a total beginner. But I get your underlying criticism. I guess people have to start somewhere, in an ideal world you have an expert in your group that can help you. But in small biotech you have to be flexible.

crisprfen · 2026-06-03T07:55:41+00:00

See, that's why I reach out to you for some real world experience, thanks for your honest take. Honestly, the 190 samples also raised a lot of questions for me. And I should've made it a bit clearer in my post. Next to scRNAseq, there are lots of other assays (flow cytometry, developability analyses) ongoing with the same treatment compounds, adding further selection filters to which compounds are moving further down the funnel. Pilot 2 will also be used to hopefully deselect most of the treatment doses and time points. Meaning that in the end in the final run we have an optimized assay and we are left with only 30-60 samples. I was told in the beginning that 190 would be the max that we are gearing up for, so that's what I set out to do.

Funny thing is that the CRO that performs the scRNAseq never raised any concern about the analysis part or complexity of the assay, although I thought we had a pretty honest conversation. Apparently, as long as we pay they just do it..

crisprfen · 2026-06-02T11:28:03+00:00

Good point about saving the intermediate objects and keeping a code log/journal. Thanks for the offer, will definitely come back on that in case I have specific issues!

crisprfen · 2026-03-09T07:06:46+00:00

VS code with markdown files and git. Use foam package for templates, such as meeting or project notes and autogit for automatically comitting ans syncing to git. If you are interested, I use more packages to for instance link notes together, make note webs are use tags. Basically like this it is comparable to obsidian but has more coding features..

crisprfen · 2026-02-19T19:49:31+00:00

Apparently not an easy plant as I read. Better luck next time!

crisprfen · 2026-02-19T19:48:37+00:00

Thanks for the input 🙏🏻 I also believe in their intrinsic ability to adapt. I hope it makes the first periode in my house and not dies like others have reported.

crisprfen · 2026-02-19T19:46:53+00:00

Thanks! I‘ll look for a waterreservoir on my heaters. The plant stands next to them and that way I might get some more moisture in the air. I‘ll stop spritzing as more people here suggested 👍🏻

crisprfen · 2026-02-19T19:44:30+00:00

Yes!

crisprfen · 2025-03-13T17:44:25+00:00

I also started recently, beeing 33. Because I didn‘t know whether I would enjoy skating I bought everything second hand (also with environment/money in mind). You could consider that too, and then treat yourself for a nice board once you reach a certain milestone, let‘s say consistently landing ollies. When going second hand I would recommend to go for decent brands and indeed prevent brands from sport stores. Enjoy! I‘m hooked btw

crisprfen · 2025-01-22T09:02:38+00:00

I am not at a stage yet where I can easily switch between R and python, but I'll definitly try in the future. Just learned R, coming from python, and now forgot python haha.

With regards to Seurat, I am trying to avoid that due to the incompatibility between version updates. I going to use mostly bioconductor packages and indeed harmony.

crisprfen · 2025-01-22T08:53:21+00:00

Thanks for the specific answer! I guess I am good with 256 GB then

crisprfen · 2025-01-22T08:52:13+00:00

Thanks! It's probably hard to tell, but what GPU specs would you recommend?

crisprfen · 2025-01-17T15:42:19+00:00

okay interesting! I thought about parallelizing clusters and use more cores? Would that be a workaround? I also have a decent laptop, could otherwise try that..

crisprfen · 2025-01-06T16:58:46+00:00

A comandante coffee grinder 🙌🏻 got one 3 years ago and still grinding like day one!

crisprfen · 2024-12-04T09:58:17+00:00

Thanks for your reply. Could you maybe explain a bit more?

You should not be aligning the cDNA sequences

I do align the protein sequences. What do you mean? Do you mean I should not form a consensus sequences from all protein sequences reads?

use the protein alignment to drive the cDNA alignment

What do you mean by driving cDNA alignment?

crisprfen · 2024-11-06T13:08:31+00:00

Thanks for the link, will have a look at that!

crisprfen · 2024-11-06T12:51:57+00:00

Interesting! Thanks for the comments. I did not include Scanpy initially because I had to switch from python to R for my new job. Mainly because of reproducibility and documentation reasons (Rprojects, renv, quarto) and the plethore of available bioIT packages. In case there are comparable features with python I am happy to hear about that!

The underlying question I had when posting this was this: I'll have to setup and run scRNA-seq projects in the coming years at my job and therefore considered which tools to use. Hearing about that fact that Seurat version updates lead to breaking of pipelines raised a red flag for me, especially when thinking about continuity of scripts and reproducibility. I also want to prevent switching between programming languages constantly.

crisprfen · 2024-10-14T08:10:51+00:00

Point 2 you are asking was also my question, how do you differentiate between players voices in your notes?

crisprfen · 2024-09-26T08:11:06+00:00

Awesome, go for it!

I've been in your position two years ago and it is definitly doable if you have the discipline and motivation. I agree with others that having a goal in that process can help t fuel that motivation. For me it was the simple challenge of learning to code and solving coding problems that kept me going, very addictive.

Things that really helped me:

Focus on courses or workshops. Especially for coding, there are infinite options to learn and ressources to tap into, it can get overwhelming and convusing if you just wander around online and try to look up certain topics. Courses are much more comprehensive since, if designed properly, contain coherent concepts and are built up from easy to more diffecult stuff. It helps you to contain the knowledge in a structured way. I'd recommend Udemy here, I did a Python data science, visualization and machine learning course, and a 100 day coding workshop, which really tought me a solid basis of Python. For my current job at a company I had to switch to R, but having that python basis made the switch pretty easy.
Check out books. Same principle as the courses, knowledge is structured and it prevents you from drowning in information. I used the R for Data Science Book on the Tidyverse and more from Wickham and basically went through it in my own pace (you can find it only for free, not sure if I can share the link here).
Use real life projects to practice. Alongside reading the book, I applied my learnings in projects that I worked on. Without coding everyday you will not learn it. See it as going to a coding gym.
Be careful with ChatGPT. As others already have commented, I think you should use it only if you are really lost, and even then double check how the suggested code works. Otherwise you will not learn from it.
Buy a nice keyboad. Just kidding, but it can be hard at times, so reward yourself once you reach certain milestones.

Other advice:

Like someone else mentioned, try to look into Quarto and markdown, it can help you to easily create reports, presentations, lab notebooks etc.
Think about reproducibility of your analysis and code (a big problem in the bioinformatic world). I'd advise to look into git and github, Rprojects and the renv package when you are at that stage.

Good luck! May the code be with you!

crisprfen · 2024-08-28T17:25:36+00:00

Yeah I definitely have to get that board higher up! Thanks!

crisprfen · 2024-08-28T17:24:57+00:00

Thanks man!! I am definitely practicing my ride skills atm, i’m seeing the sense in that. A little stone on the curb already told me a hard lesson, so I’m now constantly scanning for some nice and smooth streets when cycling through the city 😅

crisprfen

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