Running Ariana’s version which has much more stringent filtering steps before performing the WGCNA:
Removing genes that don’t show any expression (done in previous WGCNA)
Choosing how many 0s to allow per gene
Choosing expression level thresholds
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CEABiGR lncRNA - WGCNA-00
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
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CEABiGR lncRNA - RNAcentral BLASTn
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.
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CEABiGR lncRNA - DESeq2 Runs
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.
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E5 3 Species 05 - P. meandrina and P. evermanni lncRNA Discovery
lncRNA discovery completed for P. meandrina and P. evermanni
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