references genome differences

[papori]

Hi guys,

I am using 2 references genome for alignment.
I was wondering about:
Is it possible that the size/length of the chromosomes will be different between different genome references?

I found information (such as size) on the GRCh37 here:

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/

I didnt find for the HG_18_Broad_variant this info on the chromosomes size..

Thanks,
Pap

[GenoMax]

Answer for your question in bold is "likely possible" since there are multiple "patch" releases (minor revisions, if you will) for genomes.

For Example as noted for GRCh38 (this time no co-ordinates were changed but the total number of bases changed):

GRCh38.p1 is the first patch release for the GRCh38 reference assembly. No chromosome coordinates changed. This release includes 13 FIX patches and 3 NOVEL patches.

Information about the Hg18_Broad_Variant is on this page: https://browser.cghub.ucsc.edu/help/assemblies/

[Brian Bushnell]

HG18 = GRCh36
HG19 = GRCh37

They do have different lengths / coordinates. It's possible to convert between them, but better to pick one and stick with it.

[papori]

Thanks Genomax for the explain and the link!

[papori]

HG18 = GRCh36
HG19 = GRCh37

They do have different lengths / coordinates. It's possible to convert between them, but better to pick one and stick with it.

Thanks Brian!
If i understand you right:
I can use the same coordinates for both HG19_Broad_variant and GRCh37-lite?

I found this :
HG19 - This is the UCSC variant of the GRCh37 genome assembly.

In the link thar Genomax shared:

https://browser.cghub.ucsc.edu/help/assemblies/

If the HG19 is a variant of GRCh37, so the coordinates are the same?

Thanks,
Pap

[GenoMax]

@pap: Unless you are sure about the provenance you would be taking a risk transferring coordinates between two genome datasets.

[papori]

@pap: Unless you are sure about the provenance you would be taking a risk transferring coordinates between two genome datasets.

Sounds fair
Thanks!

[lh3]

If a sequence is present in both hg19 and GRCh37 (and all its patches), they have exactly the same length and coordinate. The actual sequence may be different as ucsc converted all ambiguous bases to N. There are also more sequences in GRC patches. Naming is also different.