After a meeting last week, we realized we needed to update the paper-oly-mbdbs-gen GitHub repo with the most current versions of feature files we had.
As part of that, we needed a new intron GFF file generated. I also realized that the output from the MAKER annotation from 20190709 actually has 3’/5’ UTR features, so I decided to separate those out and create separate GFFs for them, as well.
The process was performed in the following Jupyter Notebook (GitHub):
One thing to note in that Jupyter Notebook. The
complementBed command threw an error related to sorting. Two things with this:
I don’t see an issue with the sorting.
It seems to have still run just fine and generated the expected output.
Here’s quick glance at IGV visualization of the intron BED file. Things look fine.