Question: what is the difference between GRCh37 and hg19 ?
6
gravatar for jack
4.6 years ago by
jack760
Germany
jack760 wrote:

Hi all,

What is the difference between GRCh and hg? I have small RNA interaction data with genome like below and they have used hg19 for mapping the reads. I want to use GTF file in Ensemble which is based on GRCh. but I was wondering the hg and GRCh are the same? If not, where can I find the GTF file for the hg19?

chromosome  start    end      interaction ID  alignment score of target part  strand
chr2        1.9E+08  1.9E+08  human08246      32                              +
chr16       5.2E+07  5.2E+07  human04514      32                              -
chr3        1.1E+08  1.1E+08  human11115      36                              +
chrM        14360    14382    human08122      34                              +
ADD COMMENTlink modified 15 months ago by gandrescabrera80 • written 4.6 years ago by jack760
1

see: Differences Between Reference Human Genome Assemblies From Different Sources

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Pierre Lindenbaum121k

but still, I couldn't figure it out whether hg and GRCh is the same or not . could you please elaborate more ?

 

ADD REPLYlink written 4.6 years ago by jack760

Can I make a similar answer in here? Might be useful to others too. If its innapropiate take the according action to fix it, sorry.

Which is the difference between Homo_sapiens.GRCh38.91 and Homo_sapiens.GRCh38.78? Can I use a Homo_sapiens.GRCh38.91.bed as annotation to a genome referenced to Homo_sapiens.GRCh38.78?

Thanks in advance.

ADD REPLYlink modified 15 months ago • written 15 months ago by gandrescabrera80

The term "GRCh38" refers to the genomic assembly. The ".78" and ".91" refer to the version of gene annotation provided by Ensembl, i.e. where do introns/exons/etc start and end. To my knowledge, the genomic sequence for "GRCh38.78" and "GRCh38.91" should be identical and only the gene annotation should differ.

ADD REPLYlink modified 15 months ago • written 15 months ago by Manuel Landesfeind1.2k
2
gravatar for Dan D
4.6 years ago by
Dan D6.8k
Tennessee
Dan D6.8k wrote:

I believe the genomic content for the two is identical, except for the mitochondrial contig.

The contig names are also different. GRCh37 names them `chr1`, `chr2`,,`chr3`, etc, while hg19 just has `1`, `2`, `3`.

Thus you can use the same GTF file for both (excluding mitochondrial, of course) if you do a simple replace operation for the contig names.

ADD COMMENTlink written 4.6 years ago by Dan D6.8k
1

ok, thanks, so the genomic coordinates of the genes are the same in hg and GRCh ?

ADD REPLYlink written 4.6 years ago by jack760
1

and some degenerate bases have been replaced by 'N' for chr3 and chrY. see: http://plindenbaum.blogspot.fr/2013/07/g1kv37-vs-hg19.html

ADD REPLYlink written 4.6 years ago by Pierre Lindenbaum121k
1

Although this is basically true, GRCh37 has a number of patches, which won't be included in hg19.

ADD REPLYlink written 4.6 years ago by Adam990
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