Lab Notebook

TL;DR - I went through the current status of my first two chapters to get a status report of to-dos to complete rough drafts during the writing portion of today’s hack-a-thon. [Read More]

June 23 [Read More]

TL;DR - I was able to resolve the issue of all 0 count rows in the Ptuh count matrix by adding options for including multi-overlap and multi-mapping. These deviate from the default settings of FeatureCounts and I wonder if we just want to eliminate the 25 lncRNAs unable to pass these default settings. We can, however, proceed with all counts. [Read More]

TL;DR - Fixing the system environment settings for gffcompare and fixing formatting issues with out GTFs appears to have fixed issues with pipeline. The number of putative lncRNAs is now much lower (more similar to deep-dive descriptive numbers) and no duplicates are detected in bed, gtf, fasta, and count files. [Read More]

TL;DR - My students ran a variety of experiments using hairy shore crabs (Hemigrapsus oregonensis) this quarter. Some stand-out stressors were anti-biofouling paint, high temp coupled with pathogen exposure, hypoxia, NSAIDs, and caffeine. A scaled up resazurin protocol was successful as a proxy for respirometry. Use of hemocytometers, physiological assay kits, and handheld glucometers showed promise as quick and less invasive methods for measuring stress response. [Read More]