Section 2 Genome Centric Commands

Genome Centric Commands

We can interrogate the installed data in two primary ways. The first concerns data from individual genomes.

species-summary

Let's take a look at the summary of each of the two genomes that have been downloaded. Now remember that you can use the TUI here instead of the command line so that you can explore the options and what they correspond to interactively prior to trying to execute your command.

But here's my command anyway (with a placeholder for you).

elt species-summary -i <path to install> --species caenorhabditis_elegans

Repeat this for the other genome.

Question

What other summary statistics do you think would be useful to include in this output? Create a discussion topic and let us know if you have a particular request.

dump-genes

In writing this I think this subcommand is not well named. What it will actually do is export a tab delimited file listing the gene symbols, their locations within the genome etc...

But hey, let's do it anyway!

elt dump-genes -i <path to install> --species caenorhabditis_elegans 

This creates a caenorhabditis_elegans-112-gene_metadata.tsv file

Question

Should we also export gene sequences, or make that a separate subcommand? If we're going to export them should we export the full gene? The CDS? All of the CDS's for that gene? You get the picture. What would be useful to you? Create a discussion topic or vote on an already created one.