I've been tripping myself up, possibly.
The end goal is to run enrichment where the background is the uniprot Accession IDs associated orthogroups that are shared across three species of sea stars, and then the input to DAVID comparing to the background will be the uniprot accession IDs associated with unique-to-species orthogroups that are associated with DEGs.
How do I get annotation of this list of shared orthogroups? I have two versions of the table.
Orthogroup Dermasterias Pisaster Pycnopodia
OG0000000 g21735.t1, g8512.t1 g10121.t1, g10232.t1, g11028.t1, g11049.t1, g12311.t1, g12312.t1, g12494.t1, g12495.t1, g12583.t1, g12584.t1, g12589.t1, g12590.t1, g13075.t1, g13076.t1, g13077.t1, g13078.t1, g13079.t1, g13080.t1, g13081.t1, g13082.t1, g13083.t1, g13084.t1, g13085.t1, g13086.t1, g13087.t1, g13116.t1, g13117.t1, g13118.t1, g13119.t1, g13120.t1, g13121.t1, g13122.t1, g13123.t1, g13124.t1, g13125.t1, g13126.t1, g13127.t1, g13128.t1, g13129.t1, g13130.t1, g13131.t1, g13132.t1, g13292.t1, g13414.t1, g13455.t1, g13618.t1, g13756.t1, g13909.t1, g13910.t1, g1509.t1, g15496.t1, g15800.t1, g1641.t1, g1642.t1, g16693.t1, g16923.t1, g16924.t1, g16925.t1, g16926.t1, g16927.t1, g16928.t1, g16929.t1, g16930.t1, g16931.t1, g16932.t1, g16933.t1, g16934.t1, g16935.t1, g16936.t1, g16937.t1, g16938.t1, g16939.t1, g16940.t1, g16941.t1, g16942.t1, g17225.t1, g17226.t1, g17392.t1, g17393.t1, g17394.t1, g17395.t1, g18021.t1, g18022.t1, g18023.t1, g18024.t1, g18025.t1, g18026.t1, g18027.t1, g18028.t1, g18029.t1, g18030.t1, g18031.t1, g18032.t1, g18049.t1, g18050.t1, g18051.t1, g18052.t1, g18053.t1, g18054.t1, g18055.t1, g18056.t1, g18057.t1, g18058.t1, g18059.t1, g18060.t1, g18061.t1, g18062.t1, g18063.t1, g18064.t1, g18065.t1, g18066.t1, g18067.t1, g18068.t1, g18069.t1, g18070.t1, g18100.t1, g18101.t1, g18102.t1, g18103.t1, g18104.t1, g18105.t1, g18132.t1, g18184.t1, g18185.t1, g18186.t1, g18187.t1, g18188.t1, g18189.t1, g18190.t1, g18191.t1, g18192.t1, g18211.t1, g18212.t1, g18213.t1, g18214.t1, g18215.t1, g18216.t1, g18217.t1, g18218.t1, g18219.t1, g18220.t1, g18221.t1, g18222.t1, g18660.t1, g18704.t1, g18707.t1, g18708.t1, g18709.t1, g18710.t1, g18711.t1, g18998.t1, g19093.t1, g19094.t1, g19094.t2, g19095.t1, g19096.t1, g19166.t1, g19216.t1, g19217.t1, g19218.t1, g19219.t1, g19220.t1, g19221.t1, g19222.t1, g19223.t1, g19224.t1, g1948.t1, g19616.t1, g19617.t1,
Version 2 is the one shown at the top.
I have BLAST output for each species' protein lists...
I've been tripping myself up, possibly.
The end goal is to run enrichment where the background is the uniprot Accession IDs associated orthogroups that are shared across three species of sea stars, and then the input to DAVID comparing to the background will be the uniprot accession IDs associated with unique-to-species orthogroups that are associated with DEGs.
I have a table of shared orthogroups (link to table here) that looks like this:
I got this by following a script of Hollie's, that I ran in my own Rmd: project-pycno-multispecies-2023/code/27-orthofinder.Rmd.
Question:
How do I get annotation of this list of shared orthogroups? I have two versions of the table.
Version 1:
Columns are: Orthogroup; Dermasterias; Pisaster; Pycnopodia --> project-pycno-multispecies-2023/output/27-orthofinder/shared_orthogroups_all_species-wide.tsv that looks like this:
Version 2 is the one shown at the top.
I have BLAST output for each species' protein lists...
What's the best way to approach this?