Gather data (available phaeo assemblies for reference)

[maggimars]

Gather data into data directory on Poseidon:

• [x] Jgi protein models (Phytozyme gene models) for P. antarctica (CCMP1374) and P. globosa (Pg-g)
• https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=PhagloAnnotation
• https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=PhaantAnnotation
• [x] MMETSP Phaeo transcriptomes (1 globosa, 2 antarctica, 1 cordata)
• reassembled (https://zenodo.org/record/257410#.X9Jv5ulKh24) or original (https://www.imicrobe.us/#/search/phaeocystis)?
• CDS or pep?
• [x] My P. globosa (1524), P. cordata, and P. jahnii
• [x] select an outgroup and acquire reference assembly (?) for outgroup - E. hux?

[maggimars]

Answers:

MMETSP - cleaned ones from Richter - clean data for proteins

pep AND contigs/transcripts .. not CDS

jgi - filtered model transcripts, filtered model proteins

outgroup - ehux 1516 genome + diatom genome

[maggimars]

Is this what you meant by the cleaned MMETSP? https://figshare.com/articles/Data_from_The_evolution_of_silicon_transport_in_eukaryotes/12410606/1 @halexand ?

[halexand]

Ah, yes that looks similar. They are also buried on the imicrobe site. Sarah did some work figuring out how to bulk download them: https://github.com/shu251/download-cleaned-mmetsp I am not sure if they are the same but as long as we can site the dataset!

[maggimars]

OK - these are the ones they used for EukProt (links are in the datasheet: https://figshare.com/articles/EukProt_a_database_of_genome-scale_predicted_proteins_across_the_diversity_of_eukaryotic_life/12417881/2 )

If it seems right - I can just grab the Phaeo ones from here without downloading the whole dataset

[halexand]

Ah, great! Yes, that seems right then! Makes sense to just download what you need :)

[maggimars]

Regarding outgroups: JGI was down this week so I couldn't download the Ehux or diatom genomes. JGI will be back up tomorrow (Dec. 18). However, I got the feeling from the orthofinder tutorial (https://davidemms.github.io/orthofinder_tutorials/orthofinder-best-practices.html) that I might not want to include outgroups -- or I could at least compare results when outgroups are or are not included. Therefore, I went ahead with trying to run Orthofinder without outgroups.

[maggimars]

Download Ehux and Chrysochromulina genomes and transcriptomes for comparison to Phaeo in mapping results. @rondorice

[maggimars]

Micromonas

• [ ] Download all MMETSP micromonas available
• [ ] Download jgi micromonas genome
• [ ] Run orthofinder to see which transcriptome has highest overlap with genome
• [ ] use transcriptome that is most similar to genome for mapping comparison (metaT v. metaG recruitment to ref transcriptome v. ref genome)