GTF annotation for Staphylococcus aureus

Question

[Shicheng Guo]

Hi All,

Where to download GTF annotation to staphylococcus aureus?

Thanks.

[GenoMax]

Reference genome for the subspecies S. aureus aureus can be found here along with a GFF file. There are ~11000 S. aureus genomes available at NCBI so you will need to be careful about the one you are interested in.

[Shicheng Guo]

Hi Genomax, Thanks for the advice. If I want to alignment RNA-seq data to staphylococcus aureus genome, what's the correct way I should do? current I just alignment the RNAs-seq reads to NC_007795.1

[GenoMax]

You can. Remember that bacterial RNAseq should be much simpler. No splicing to worry about.

Answer 1

[lieven.sterck]

If you don't find it right away you're probably best to download the gff version (eg from : https://www.ncbi.nlm.nih.gov/nuccore/NC_007795.1 ) and then convert it to GTF (eg with gffread from Cufflinks).