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

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

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.

ensembl next-gen rna-seq genome ucsc

1 answer

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 ...

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