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]
BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit
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]
Re-run Trinity with correct files
Today I re-ran Trinity because the original files I used that I downloaded to my computer from nightingales were too small and not .fastq.gz. Sam showed me how to do rsync from nightingales to mox. I also am working on doing a BLAST with the finished Trinity.fasta that is too... [Read More]
Sent First Trinity Assembly Job to Mox!
Today, with Steven’s guidance, I sent the first job to mox! I am not sure if it will work, but I have it set up to get email notification when the job finishes. Below I provide the link to the .sh script to run Trinity as well as the command... [Read More]