Creating PCAs

Alright, as of last time, our general goal was to do the following (along with a few other priorities): Track down data on infection level of crabs over time, and plot For each of our three transcriptomes, make a PCA with one point for each library. See if points cluster together by day, temperature, infection level (from qPCR data), and crab. This will be done using DESeq2 Align crabs D and F to hemat_transcriptomev1.6 and cbai_transcriptomev2.0. This should just check whether our alignment works well – since these are uninfected crab, we shouldn’t get any alignments to hemat_v1.6, and the alignment to cbai_v2.0 (which is unfiltered) should give an idea of the accuracy of our filtering for cbai_v4.0 (which is filtered to exclude all non-bairdi sequences). Write a blog post on the bittercrab website We can check off number 4 – take a peek here! The rest of the entry…

from Aidan F. Coyle