Getting ready to run some qPCRs and first we need to confirm that our RNA is actually DNA-free. Before we can do that, we need some primers to use, so I decided to semi-arbitrarily select three different gene targets from our MEGAN6 taxonomic-specific Trinity assembly from 20200122.
I used our recent differential gene expression analysis to identify those genes which were highly differentially expressed in infected vs. uninfected samples.
Overall, the process went something like this:
- Sort upregulated genes in infected group by logFC (fold change) to find Trinity transcript IDs of highly expressed genes:
awk 'NR>1' salmon.gene.counts.matrix.infected_vs_uninfected.edgeR.DE_results.P0.05_C1.infected-UP.subset \ | sort -n -k4,4
- Search for some of the highly expressed Trinity IDs in the Trinotate annotations to find SwissProt IDs:
grep "TRINITY_DN6549_c0_g1" \ 20200126.cbai.trinotate_annotation_report.txt