Today I attempted to take my BLAST output on Hummingbird and work through this blast-2-slim notebook of Steven’s. I had gone through this before using Cgigas. I got stuck today at the part where you !join _blast-GO-unfolded.sorted with GO-GOslim.sorted. Will ask tomorrow. Additionally, today I worked on using transrate to...
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BLAST really running on Mox, 2015 Oysterseed new plan
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...
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Sent BLAST to Mox, and Plan for rest of Week
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!...
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Trinity failed; Re-run, and Notes from Crab Meeting
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.
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November Goals
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...
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