Lab Notebook

Running individual WGCNA analyses on male and female sets of oysters. Initial code can be found here. General notes about first run: Using signed networks (those that take into account the direction of expression as well as the value of the count - up or down) Blockwise clustering for module formation, usually good for large datasets, probably not necessary since there isn’t too much data Current status: Switched from this analysis at module merging stage since none of the modules merged with a stringent similarity setting [Read More]

Started with a couple smaller datasets included in the umbrella of RNAcentral, but got almost no hits so scaled up. Blasted the entire RNAcentral database (over 3 million sequences) with the Crassostrea virginica lncRNA FASTA file. [Read More]

Ran DESeq2 for females only, males only, and combined not accounting for sex. Volcano plots, PCAs, and heatmaps of the top 30 most differentially expressed included for each. [Read More]

lncRNA discovery completed for P. meandrina and P. evermanni [Read More]

Ran HISAT2 alignments for Pocillopora E5 data using P. effusa and P. verrucosa references. P. effusa had the worst alignment. P. verrucosa and P. meandrina are very similar in alignment rates, so we will go with P. meandrina since it has a better annotation. [Read More]