I sent a
.sh to Mox to perform a BLAST with my assembled C. bairdi transcriptome and swiss prot. I am also working on figuring out how to do this on Hummingbird (on
toaster/grace). Additionally, I have come up with a list of things I want to accomplish this week!
BLAST to Mox
Yesterday I wasted a bunch of time trying to figure out how to run Jupyter on Mox in order to perform a BLAST… totally forgot that you can just do:
sbatch -p srlab -A srlab shell.script while logged in to Mox…
So today, I got some assistance from Steven and Sam to make sure that my 20181106_Cb-sprot_blast.sh will work (GitHub Issue # 470).
Script lives on Mox in
/gscratch/srlab/graceac9/jobs/ and also a copy of it is here.
The job is officially in queue (# 428276).
Plan for the rest of the week (non-class-related tasks):
- Run Bioanalyzer on what I extracted last week using the Qiagen RNeasy Micro Plus Kit
- Get input from Emma on my error rate determination of her Skyline file (she’ll come by between 12:30 and 2:30 pm)
- Try BLAST on Hummingbird
- Edit and publish Crab Meeting #6 DecaPod episode (at home in evening)
- Work on R script for organizing new Qubit data
- Come up with an extraction plan to finish by Dec 21st (when I leave for Holidays)
- Determine how many kits need to order
- Extract RNA using Qiagen RNeasy Micro Plus Kit from a subset of the samples I selected Wednesday
- Check in on BLASTs
- START WORKING ON GSS POSTER!!! GSS is Thurs Nov 15th