Using C. bairdi transcriptome v4.0

Recap Last time, I described aligning all libraries to the Hematodinium-specific transcriptome hemat_transcriptomev1.6 and running them through my pipeline (kallisto -> DESeq2 -> GO-MWU). I made two comparisons – Ambient Day 2 vs. Elevated Day 2 and Elevated Day 0 vs. Elevated Day 2 (reminder: Day 0 samples were taken when all crabs were still at ambient temp). Since then, I repeated the same process, but with a C. bairdi – specific transcriptome, cbai_transcriptomev4.0! I made the same two comparisons as before. Scripts are noted with a prefix in the 40s. Prior to aligning libraries, I first built an index – that process is shown within the scripts. Scripts available as follows: Creating BLASTx index for cbai_transcriptomev4.0 Running kallisto Running DESeq2 Obtaining GO terms Preparing one of the inputs for GO-MWU Preparing the other input for GO-MWU Running GO-MWU Again, two comparisons were made – Elevated Day 0 vs. Elevated…

from Aidan F. Coyle