difference between b37 and hg19

[Bogdan Tanasa]

Dear all,

I found some publications that released the data by using b37 genome coordinates ...

are these identical to hg19 coordinates ? is there any liftOver necessary ? thank you,

-- bogdan

[Bogdan Tanasa]

And I could also add please : what are the differences between b37 genome assembly and GRCh37 ?

[Steve Heitner]

Hello, Bogdan.

I believe you will find the following resources helpful:

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/HOIDP_EodqA/cskWIo4yWVwJ

https://answers.dnanexus.com/p/183/

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

---
Steve Heitner
UCSC Genome Bioinformatics Group

--

[Bogdan Tanasa]

Thank you Steve ! Briefly, if you could please clarify :

the coordinates of hg19 are identical with the coordinates of b37, and therefore no liftOver is neccesary ?

an answer of the type "yes/no" would be really appreciated ;) thank you again very much,

-- bogdan

[Steve Heitner]

Hello, Bogdan.

In terms of a simple yes/no answer, the answer is no.  They are mostly the same, but there are differences which are expanded upon in the resources I included in my initial response.  More importantly, if you are trying to use b37 with UCSC software or hg19 with GATK, you will most likely run into difficulties because of differences in the naming conventions between hg19 and b37.

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[Bogdan Tanasa]

HI Steve,

thank you for the quick response. If I may add a little note : the article " A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping." released a large dataset of 3C interactions :http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525 .

their coordinates are b37, our coordinates are hg19. Of course, the naming convention for chromosomes not a problem.

the question arises when converting the coordinates from b37 to hg19. As the mitochondrial genome is not an issue, I would think that most of the coordinates would be the same between b37 and hg19 ? thanks,

-- bogdan

[Steve Heitner]

Hello, Bogdan.

If the mitochondrial sequence and the differences in naming convention are not of concern to you, then the coordinates should be the same between both assemblies.

All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.