Biologist in bioinformatics
Hello people of Reddit, i seek your advice, and generally just feel like getting this out of my system. (It did get a bit long and messy, just like my code tends to, sorry.)
I am feeling increasingly lost in my post-PhD limbo. (Defended 8mo ago, neuroscience.) I am in a weird (but not unique) position of having been "forced" (ie. "Well , someone has to do it!! :D") to analyse genomic/single cell omics data for YeArS during PhD with a better-than-average stats/linear algebra base (good stats teacher during my uni years) and no mentorship. Learned (still learning...) it from scratch, trial/error, digging up tutorials and Biostars. Never had a mentor who knew anything about it, our lab was a vey small, classic post mortem human histology lab.
I do have fun with the analysis, its like detective work, but I obviously never got to the level of actual computational scientists. Like, to this day I struggle with git and anything I need the terminal for. And it tires me a lot too. Its not my domain - my home is the lab, the confocal, the relatively basic stats of my primitive little data...
However, I quickly realized that omics analysis became my "most valued" skill. Before even finishing PhD i have been asked to join 2 labs (both part-time), 100% for single cell data analysis and related things. And while I am SUPER GRATEFUL for the opps, I
1, feel horrible all the time due to not being entirely sure about what I'm doing - and seeing clearly that even the best I do will only ever be mediocre. Because clearly I am not at the level of comp bio ppl regularly doing Nature Neuro level analyses.
2, i feel like I am a Temu bioinformatician for these labs. Cheap, but .. 🥲😂
3, i am truly unable to decide whether this is GOOD because I will get better and better and easly build up an 8+ year practical experience in biologically interpreting messy omics data from mice, human, retina, brain, etc, and in bridging communication between comp guys and non-comp guys, which is clearly a very valuable thing ...
OR...
I am wasting my time and even doing damage to my current PIs because I deliver objectively mediocre results; I will never be good enough to apply to "BETTER" labs (I mean regarding single cell omics); my knowledge will plateau; and I will lose touch with my original (albeit basic) expertise.
How do you see this, people in bioinformatics? What is the "general opinion" about people who transition from biology to bioinfo/comp bio? Is there a role for "people like me"?
To give you a snapshot of my current "skills", I use R and the Seurat/Bioconductor world, usually use Harmony for integration, and my fun starts at cluster identification/DEG interpretation/pathway analyses. I shuffle multiple approaches for DEG testing - it also depends on the dataset/our questions. I prefer pseudobulk but I also check what Seurat does with default Wilcox and MAST. I use DecontX and SoupX (compare), scDblFinder, and cell type score based manual filtering for cleaning up data. I use monocle3 for pseudotime inference, but for example, velocity is intimidating for me. I have some experience with cellranger and building custom reference genomes, but that is way out of my comfort zone. I recently started to work on spatial data and for that i use the python/scanpy world l, which is less comfortable than R at this point, but its not as bad as I feared it would be.
Also... I do think a lot about applying for postdocs, but I have quite low self-esteem and am not very ambicious. I believe for a succesful postdoc period, you Need To Want To Be A Postdoc 100000%. I don't dream of establishing and maintaining my own lab, I think i'm rather a staff scientist/happy cog in the machine type... Also as a female approaching 30, the kid question looms over me, among many other looming things, not making any decision particularly easier...
SOOOO .. i'd be very grateful for any insight, advice, anything .. ✌️🙆♂️