See that link for run setup and configuration.
Before proceeding further, it should be noted that I neglected to provide Maker with a transposable elements FastA file for RepeatMasker to use.
The following line in the
maker_opts.ctl file was originally populated with an absolute path to data I didn’t recognize, so I removed it:
repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner
I’m not entirely sure what the impacts will be on annotation, so I’ve re-run Maker with that line restored (using a relative path). You can find the results of that run here:
Annotated genome file (GFF):
I’d like to post a snippet of the GFF file here, but the line lengths are WAY too long and will be virtually impossible to read in this notebook. The GFF consists of listing a “parent” contig and its corresponding info (start/stop/length). Then, there are “children” of this contig that show various regions that are matched within the various databases that were queried, i.e. repeatmasker annotations for identifying repeat regions, protein2genome for full/partial protein matches, etc. Thus, a single scaffold (contig) can have dozens or hundreds of corresponding annotations!
Probably the easiest and most logical approach from here is to start working with scaffolds that are annotated with a “protein_match”, as these have a corresponding GenBank ID. Parsing these out and then doing a join with a database of NCBI protein IDs will give us a basic annotation of “functional” portions of the genome.
Additionally, we should probably do some sort of comparison of this run with the follow up run where I provided the transposable elements FastA file to see what impacts the exclusion/inclusion of that info had on annotation.