Question: What Is The Difference Between Hg18 And Hg19?
14
gravatar for Sara
6.8 years ago by
Sara160
Sara160 wrote:

Hello

what is the difference between hg18 and hg19?

Thanks

Sara

genome hg • 45k views
ADD COMMENTlink modified 6.8 years ago by Jorge Amigo11k • written 6.8 years ago by Sara160
6
gravatar for Biomed
6.8 years ago by
Biomed4.4k
Bethesda, MD, USA
Biomed4.4k wrote:

These are the names/versions of human genome references as used by UCSC browser. They are generally counterparts of NCBI 36 and 37. The current one is hg19 (Human Genome version 19). http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/

ADD COMMENTlink written 6.8 years ago by Biomed4.4k
3

@sara I would strongly recommend to remap the reads instead of running liftover.

ADD REPLYlink written 6.8 years ago by lh331k

Why? And what is the best/most efficient way to do so?

ADD REPLYlink written 6.4 years ago by bp0

Thanks for reply. I would like to know if i mapped the reads on hg18 and the same at hg19 what will change? Thanks

ADD REPLYlink written 6.8 years ago by Sara160

A great number of your genomic coordinates would change between the two mappings. To convert between the two, you can use the liftOver tool: http://genome.ucsc.edu/cgi-bin/hgLiftOver

ADD REPLYlink written 6.8 years ago by Chris Miller20k

I am not aware of a list of all the changes (a diff) between the two builds. One imagines that one can parse the two fasta files to compare and contrast the two builds. You can also use a tool called liftOver from UCSC to "lift" coordinates between the two builds. As liftOver reports its failures, that gives you a rough feeling about if the region pretty much stayed the same or changed (i.e deleted from the other etc)

ADD REPLYlink written 6.8 years ago by Biomed4.4k

I agree with @Ih3

ADD REPLYlink written 6.8 years ago by Biomed4.4k

it is definitely worth it

ADD REPLYlink written 6.8 years ago by Jorge Amigo11k
5
gravatar for Jorge Amigo
6.8 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

if you are asking for the difference in the content, hg18 (or NCBI36, hg18 is just the UCSC's nomenclature) is an older version of the human genome from ~2006, and hg19 (or GRCh37, hg19 is just UCSC's nomenclature again) is the a newer one which I'm almost certain that it was first released on ~2009, although the ongoing work doesn't seem to have ended and subversions have been published since then. if you want to check yourself for differences, you can go to the GRC human genome website and play with the assembly combo box, watching how the gaps are being covered from older to newer versions.

but as I have read on other answer's comments, if you are asking this because you are considering your options for a short-read alignment, I would definitely not go for hg18. don't forget that what you sequence is real genome, and in order to obtain the most accurate alignment you should always use all the genome knowledge available, the most accurate template for your alignments. that is hg19.

ADD COMMENTlink written 6.8 years ago by Jorge Amigo11k
2
gravatar for Malachi Griffith
6.8 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

If you are generally interested in what changed from hg18 (build36) to hg19 (build37), you can also refer to this discussion here: difference-between-ncbi-build-36-3-and-ncbi-build-37-1

ADD COMMENTlink written 6.8 years ago by Malachi Griffith17k
2
gravatar for Obi Griffith
6.8 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

Another important difference which I believe first appeared in hg19 was the inclusion of alternate haplotype assemblies for chr6 (7 haplotypes), chr4 (1 haplotype), and chr17 (1 haplotype). This is important because if you are doing an alignment against hg19 and your sequences come from one of these regions with alternate haplotype assemblies you can get a new kind of (apparently) ambiguous alignment where your sequence aligns equally well to chr6 but also chr6_apd_hap1, chr6_cox_hap2, etc. This may cause problems in existing scripts that are not aware of this issue.

https://lists.soe.ucsc.edu/pipermail/genome-announce/2009-April/000161.html

http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=242782529&clade=mammal&org=0&db=0

ADD COMMENTlink written 6.8 years ago by Obi Griffith17k
0
gravatar for Greg Tyrelle
6.8 years ago by
Greg Tyrelle70
Netherlands
Greg Tyrelle70 wrote:

The only difference I know between the GRCh37 (b37) build and hg19 is for chrM. See here:

https://lists.soe.ucsc.edu/pipermail/genome-announce/2009-July/000169.html

ADD COMMENTlink written 6.8 years ago by Greg Tyrelle70
2

that's between different "revisions" of hg19, no?

ADD REPLYlink written 6.8 years ago by brentp22k

It was a release timing issue for UCSC, rather than a difference between revisions.

ADD REPLYlink written 6.8 years ago by Greg Tyrelle70
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