Is there any differences between Human Genome downloaded from UCSC website and the on from Ensembl

Question

[Y Tb]

I am trying to use tophat to map RNA-seq data with human genome, I found that the human genome and different versions from annotation files are available under the tab Index and annotation downloads at the tophat website as shown in the table below:

Data source    Version    Size        Last Modified
Ensembl        GRCh37     17297 MB    5/14/2015 17:23
UCSC           hg18       17349 MB    5/14/2015 15:31
               hg19       21058 MB

• GRCh37 link: ftp://igenome:[e-mail]/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz
• hg18 link: ftp://igenome:[e-mail]/Homo_sapiens/UCSC/hg18/Homo_sapiens_UCSC_hg18.tar.gz
• hg19 link: ftp://igenome:[e-mail]/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz

The question here, is there any differences between human genomes GRCH37 from Ensembl and hg19 from UCSC?

I know that the annotation files are different, but I am not sure if the genomes are the same or not.

Answer 1

[Pierre Lindenbaum]

Yes there are some slight differences (degenerate bases, chromosome names... ) : the see http://plindenbaum.blogspot.fr/2013/07/g1kv37-vs-hg19.html , Chry In 1000G Vs Hg19 ...