Here’s what Steven and I talked about and what I’ll focus on after I send out my RNA.

Here’s the post from yesterday where I laid out the agenda items: Here

TLDR: What I’ll Aim To Have by Next Week:

  1. A list of the head of all the files I have from collaborators related to each species in the readme of the repository
  2. Count matrices that I trust from each species
  3. BLAST outputs from the augustus.codingseq.aa or equivalent files from each species
    i. join the BLAST ouptut with the count matrices

Also: Apply to funding from the College of the Environment for Conference Travel: DUE JULY 11

Notes on what we talked about:

For Each Species:

  • Align data to respective genomes
  • Get count matrices
  • Annotate

BLAST to uniprot → https://github.com/grace-ac/paper-pycno-sswd-2021-2022/wiki/Key-Files
augustus.hints.aa

g3450.t1
MNYRTDDEIYEDEVDEETKLHHRIDERGVNGTDSRDEPTRVPPAKQLKIQAPVLASRLQLEAVRRPHPPPLHPPQIHLYLEPHLEALQQRCDSYKGIVG*

  • Join with count matrix → this will functionally annotate it
  • Make sure each count matrix has fasta file that has same gene name that can be joined