When writing scientific names: italicize family, genus, species, and variety or subspecies. Begin family and genus with a capital letter. Kingdom, phylum, class, order, and suborder begin with a capital letter but are not italicized.
Here is the complete taxonomy:
NCBI’s fastq-dump has to be one of the worst-documented programs available online. The default parameters for fastq-dump are also ridiculous and certainly not what you want to use. They also have absolutely required parameters mixed in with totally optional parameters, and so you have no idea what is required and what is optional. Here, we take a look at some of the options and hopefully help you decide which parameters to run.
Not all the options available to fastq-dump are listed on the NCBI website. It is not a very well documented program! Here is the current list.
If you have a genome annotated in RAST and you want to create a genome scale metabolic model, here is one way to do it using PyFBA and the SEED.
Just a short note so we can remember how to remove excess (old) kernel packages from an Ubuntu installation.
The sequence read archive (aka short read archive) SRA metadata is complex! This is a brief guide to help you navigate it.
One key thing to remember is that:
A project (SRP) has one or more samples. However, projects are in the table called study.
A sample (SRS) has one or more experiments (SRX).
An experiment has one or more runs (SRR).
What you really want are the runs, and this is how you can get them!
We use git branches to manage our software. These notes show how we merge and manage branches to release updates to our software.
Searching with bowtie Creating indexed bam files from sam files is something we need to do all the time. This is just a hand full of simple commands to remind you how to do that.
We also use the PySAM module to extract some information about the alignments.