ValWood
commented
2 years ago Hi,
There are 397 features in this file. Some of them appear to be already annotated but some appear to be in contigs that we have not hosted (I can't remember what the decision was about this but there were 1000's of contigs If I remember correctly so I think we maybe only hosted contigs with annotated features).
What we would need is a mapping of these features to the Japonicus systematic IDs so that we do not create any duplicate features (maybe Liz can supply this?)
For example,
Tj10_partial_retrotransposon-10.1 | supercont5.10 | 331 | 5220 in the spreadsheet is SJATN_00206
snezhkaoliferenko
@ValWood @kimrutherford
Hey guys,
I'll reply to your other messages shortly (sorry for being a bit tardy but it's not good time for me at the moment, I feel like am behind on everything). Here I thought to ask how we deal with new element IDs. I am now curating https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010100 and they mention: "Multiple-sequence alignment of these regions allowed us to identify 10 new retrotransposon families, that we have named Tj12 to Tj21 (Table S2).
Could we assign those?
Thank you! S.