What Is The Difference Between GRCh37 And Hg19 ? - BioStars

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Latest Open Jobs Tutorials Tags About FAQ Community Planet New Post Log In New Post Latest Open News Jobs Tutorials Forum Tags Planet Users Log In Sign Up About what is the difference between GRCh37 and hg19 ? 2 13 Entering edit mode 11.0 years ago jack ▴ 990

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 + RNA-Seq Assembly genome alignment • 48k views ADD COMMENT • link updated 3.8 years ago by Ram 45k • written 11.0 years ago by jack ▴ 990 3 Entering edit mode

see: Differences Between Reference Human Genome Assemblies From Different Sources

ADD REPLY • link 11.0 years ago by Pierre Lindenbaum 167k 0 Entering edit mode

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

ADD REPLY • link updated 3.8 years ago by Ram 45k • written 11.0 years ago by jack ▴ 990 0 Entering edit mode

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 REPLY • link 7.7 years ago by gandrescabrera ▴ 80 0 Entering edit mode

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 REPLY • link 7.7 years ago by Manuel Landesfeind ★ 1.4k 0 Entering edit mode

In GRCh37.91, what does that .91 mean?

ADD REPLY • link 6.3 years ago by morshed9642 • 0 0 Entering edit mode

see C: what is the difference between GRCh37 and hg19 ?

ADD REPLY • link updated 6.3 years ago by ATpoint 90k • written 6.3 years ago by Pierre Lindenbaum 167k 0 Entering edit mode

Hi Pierre..thanks for the link...I am sorry that I am still confused because when I google GRCh37.91, it does not show up...that ''.91'' comes along only with GRCh38. I understand that GRCh37 is the older version than GRCh38. But is that '0.91' a 'Patch'? If so, can it be used for both GRCh 37 or GRCh38?

Thanks for your help

ADD REPLY • link 6.3 years ago by morshed9642 • 0 0 Entering edit mode

Hi Pierre..thanks for the link...I am sorry that I am still confused because when I google GRCh37.91, it does not show up...that ''.91'' comes along only with GRCh38. I understand that GRCh37 is the older version than GRCh38. But is that '0.91' a 'Patch'? If so, can it be used for both GRCh 37 or GRCh38?

Thanks for your help

ADD REPLY • link 6.3 years ago by morshed9642 • 0 4 Entering edit mode 11.0 years ago Dan D 7.4k

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 COMMENT • link 11.0 years ago by Dan D 7.4k 2 Entering edit mode

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 REPLY • link 11.0 years ago by Pierre Lindenbaum 167k 1 Entering edit mode

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

ADD REPLY • link 11.0 years ago by jack ▴ 990 1 Entering edit mode

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

ADD REPLY • link 11.0 years ago by Adam ★ 1.0k 3 Entering edit mode 6.0 years ago Kevin Blighe ★ 90k

More information to add (courtesy MatthewP): GRCh37 / hg19 / b37 / humanG1Kv37 - Human Reference Discrepancies

In essence: GRCh37 is identical to hg19 on the main contigs (chr1-24), but differ on chrM.

Kevin

 ADD COMMENT • link 6.0 years ago by Kevin Blighe ★ 90k

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