Functional annotations GFF file - Githubissues

snayfach / UHGV

Unified Human Gut Virome Catalog

https://portal.nersc.gov/UHGV

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Functional annotations GFF file #16

Closed snayfach closed 1 year ago

snayfach commented 1 year ago

Done

[x] product when eggNOG is missing
[x] drop NAME field: ID=UHGV-0108331_4;Name=UHGV-0108331_4
[x] copy to FTP location and open permissions
[x] document files
[x] alternate (11)
[x] "PhANNs = HTJ: HTJ"
[x] fix reference id column
[x] change partial to yes/no
[x] add PHROG category
[x] standard vs alternate genetic code
[x] include description with db_refs
[x] change ncRNA to tRNA
[x] drop hypothetical product
[x] add Name attribute

To do

[ ] how to split types into separate tracks in geneious
[ ] make sure genes in correct order
[ ] add pangenome frequency and category
[ ] indicate if is a marker gene (and at what rank)
[ ] label genes with stop codon read throughs
[ ] label viral and non-viral genes?
[ ] add CRISPR array track
[ ] add gc skew
[ ] add defense system track
[ ] color genes by PHROG category (geneious assigns random colors to unique values)
[ ] label terminal repeats