Today I’m trying to get started on the new BLAST +2.81 that has new databases and improved performance. This is pretty exciting because once I figure out how this works, I’ll be able to easily get taxonomy information like Order, Class, etc. I’m attempting what I believe is the first...
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Error 3 on Centrifuge- Couldn't finish Extraction with TriZol LS Reagent
Today I tried out the Trizol LS Reagent extraction, but the centrifuge in the 4˚C in FTR 213 had an “Err 3” message, which happens when there’s an error in the rotational speed measurement system (GitHub Issue #542). I’ll put a different centrifuge in the 4C and re-try the protocol...
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2015 Oysterseed DIA MSStats Figures Progress
Today I went through my R script for the RobertsLab/project-pacific.oyster-larvae project. I have a Volcano Plot and a Comparison Plot. I also did some data process plots: Profile Plots and QC Plots. I am working on updating the MS Stats protocol, and will include all the resources I used to...
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January 2019 Goals
2015 Oysterseed DIA
Finish data analysis
Edit paper with new methods, etc.
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BLAST nt taxonomy with C bairdi had no taxonomy data
Today I checked on my finished BLAST on Mox with my assembled C. bairdi transcriptome and the nt taxonomy database. It finished after three-ish days, and the file was large. However, all of the taxonomy cells were “N/A”. I made a GitHub Issue, and got some input and am now...
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