How to (and where) download Zebrafish Reference Genome (other than Ensembl or USCS)?

Question

[realnewbie]

Hi, I need to downlaod a reference genome file for zebrafish genome. I have tried the recent assembly (GRCz11) from Ensembl and USCS (in compressed file format, fa.gz). The thing is the file I have downloaded from USCS did not work in STAR Aligner. In addition, there is no such file in Ensembl including all the chromosomes in one file, they are all seperate. The problem is that I am not a RNA-seq expert, and I am not sure to add all the fasta files of chromosomes in one file and use it. I am not sure whether it will work or not. My question is, do you know any other database that I can download the primary assembly file of zebrafish genome (all chromosomes in one fasta file). If not, what would your suggestion be? Many thanks!

[GenoMax]

Make this easy on yourself and download sequence/index/annotation bundles for Danio from Illumina's iGenomes site.

[A. Domingues]

This is usually good advice, but as of today, GRCz11/danRer11 is not available as a bundle, so it doesn't help the OP.

Answer 1

[WouterDeCoster]

The thing is the file I have downloaded from USCS did not work in STAR Aligner.

What does that mean? You have to be more specific.

In addition, there is no such file in Ensembl including all the chromosomes in one file, they are all seperate.

ftp://ftp.ensembl.org/pub/release-93/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz

The problem is that I am not a RNA-seq expert, and I am not sure to add all the fasta files of chromosomes in one file and use it.

That would by okay.

[realnewbie]

I got my mistake. As it was stated on the Intro2RNASeq as "UCSC and Ensembl differ in their naming conventions and the frequency of updates", it is important to use same files from same browser and so on. It is also possible to download recent zebrafish genome assembly and annotation files from here: Ncbi genome Many thanks to all.