Lab Notebook

Today I officially ran BLAST on Mox. It kept failing the past couple days, and Steven pointed out I didn’t actually make the directory I was telling Mox to put the output in, and that I was saying to use blastn when it should have been blastx. I also met... [Read More]

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!... [Read More]

Trinity My Trinity job failed and it turns out it’s because I was missing a \ after /gscratch/srlab/programs/Trinity-v2.8.3/Trinity. I fixed that and then re-sent the job to Mox. The new script is called 20181101_Cbairdi_trinity.sh and it lives in my /gscratch/srlab/graceac9/jobs/ directory on Mox. [Read More]

Crab Project RNA extractions and Libraries (Get this done before I go home Dec 21st) Come up with RNA extraction plan for the remaining libraries Perform extractions using Qiagen RNeasy Plus Micro Kit Data organization Create new R scripts for adding new Qubit results data to a master file combining... [Read More]

Today I ran BLAST with the bad fasta from the Trinity run from last weekend. Will look more at the notebook Steven sent me to do the BLAST stats, goslim, contigs, go slim tables, etc. I also have been getting some input from Sam as to how best to manage... [Read More]