STEP# 1: Get proper resources for working on genome of interest

It is typical that you get a basic set of genome data for any organism with which you’ll be working. By way of example, in preparation for today we’ll get a file that includes the sequence of the entire budding yeast genome.

Illumina’s iGenomes site is a collection of reference sequences and annotation files for commonly analyzed organisms. Importantly, many of these are in multiple forms and can save you conversions at times. You’ll see today file conversions are very common, and obviating the need for more can be a welcome convenience.

We’ll get the information that corresponds to the current version available from the UCSC Genome Bioinformatics for the budding yeast Saccharomyces cerevisiae. Download sacCer3 from the iGenome site.

wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/UCSC/sacCer3/Saccharomyces_cerevisiae_UCSC_sacCer3.tar.gz

And unpack it.

tar xzf Saccharomyces_cerevisiae_UCSC_sacCer3.tar.gz

(OPTIONAL) We’ll clean up a bit by deleting the gzipped file we downloaded. Plus the IGenomes README.txt also because soon we’ll have lots of files in our working directory.

rm Saccharomyces_cerevisiae_UCSC_sacCer3.tar.gz
rm README.txt

We’ll need the sequence of the entire genome in fasta form and so we’ll pull that out of the large collection of files for yeast, copying it to our current directory. The current directory is designated by the dot Unix shortcut at the end of the command below.

cp Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa .

We’ll do likewise for another form of the genome information.

cp Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa.fai .

(OPTIONAL) We have what we need but let’s just put all the yeast data somewhere out of the way so we have it if we need it but it isn’t cluttering our working directory.

mv Saccharomyces_cerevisiae /usr

Verify when that is all set by checking directory.

ls

Alternatively, you can use rsync to go obtain these files directly from UCSC Genome Bioinformatics.

In a browser you can download here or do via FTP here. The fasta file from there seems to require additional conversion, see the about twoBitToFa here