Lab Notebook

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]

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]

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]

Today I worked more on my R script for adding new Qubit files. Everything works great up until the actual joining of files. After joining, there are extra columns that have the extensions “.x” and “.y”… I think it has something to do with the fact that some columns are... [Read More]

Today, Steven, Sam, and I discussed where we’re at with the crab samples and RNA extraction. We decided to extract some samples using the RNeasy Mini Plus Kit from Qiagen that Sam has already used and had decent results. In the meantime, I’ll be working on creating a little metadata... [Read More]