Tutorial

Once you have the dependencies installed, it's time to actually annotate something! This guide will take you through a short example on some test data.

See this workshop tutorial for further practice with using dammit for annotating a de novo transcriptome assembly.

Data

First let's download some test data. We'll start small and use a Schizosaccharomyces pombe transcriptome. Make a working directory and move there, and then download the file:

mkdir dammit_test
cd dammit_test
wget ftp://ftp.ebi.ac.uk/pub/databases/pombase/OLD/20170322/FASTA/cdna_nointrons_utrs.fa.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/pombase/OLD/20170322/FASTA/pep.fa.gz

Decompress the file with gunzip:

gunzip cdna_nointrons_utrs.fa.gz pep.fa.gz

Databases

If you're just starting, you probably haven't downloaded the databases yet. Here we'll install the main databases, as well as the eukaryota BUSCO database for our yeast dataset. This could take a while, so consider walking away and getting yourself a cup of coffee. If you installed dammit into a virtual environment, be sure to activate it first:

dammit databases --install --busco-group eukaryota

Alternatively, if you happen to have downloaded many of these databases before, you can follow the directions in the databases guide.

While the initial download takes a while, once its done, you won't need to do it again. dammit keeps track of the database state and won't repeat work its already completed, even if you accidentally rerun with the --install flag.

Annotation

Now we'll do a simple run of the annotator. We'll use pep.fa as a user database; this is a toy example, seeing as these proteins came from the same set of transcripts as we're annotating, but they illustrate the usage nicely enough. We'll also specify a non-default BUSCO group. You can replace the argument to --n_threads with however many cores are available on your system in order to speed it up.:

dammit annotate cdna_nointrons_utrs.fa --user-databases pep.fa --busco-group eukaryota --n_threads 1

This will take a bit, so go get another cup of coffee...