This is an awesome pipeline! One additional suggestion would be to provide some summary stats for how many / what percent of genes and isoforms were annotated to the different databases (perhaps also including some way to quantify real annotations vs "uncharacterized protein", etc) . Also, including some code for how to convert the final parsed .csv file dammit contig IDs to the original Trinity contig names would be really useful.
This is an awesome pipeline! One additional suggestion would be to provide some summary stats for how many / what percent of genes and isoforms were annotated to the different databases (perhaps also including some way to quantify real annotations vs "uncharacterized protein", etc) . Also, including some code for how to convert the final parsed .csv file dammit contig IDs to the original Trinity contig names would be really useful.