Question: Comparing genome assemblies
1
gravatar for xandinho2468
3.5 years ago by
xandinho246820
Munchen
xandinho246820 wrote:

I have a list of Refseq IDs from Vv genome that came from a Pullseq analysis experiment. I need to convert them to ensemble ID that comes from the consortium. I the past I used GFFcompare to retrieve the list but in this case now only the NCBi reference is different but also the number of predicted genes is different.

Is there a way to compare the two assemblies or to "translate" the coordinates from one ref to the other?

id genome • 1.2k views
ADD COMMENTlink modified 3.5 years ago by Denise - Open Targets5.0k • written 3.5 years ago by xandinho246820
1

What is Vv genome? You know but we don't :-)

ADD REPLYlink written 3.5 years ago by genomax73k
1

Vv genome means - vaccinia virus genome???

ADD REPLYlink written 3.5 years ago by Naresh60
1

Vitis vinifera. sorry!!!

ADD REPLYlink written 3.5 years ago by xandinho246820
1

If the assemblies are different then short of doing alignments it would not be possible to translate the coordinates directly (unless Ensembl or NCBI has already done this step).

ADD REPLYlink written 3.5 years ago by genomax73k
1
gravatar for Denise - Open Targets
3.5 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

The chances are that the RefSeq IDs will be the same across the two assemblies. The coordinates of the genes will change when comparing two assemblies, A and B. But it's unlikely new IDs will be given to the same gene in the two different assemblies. So if you have a list of RefSeq IDs e.g. NM_001281185, you can convert them into Ensembl IDs using BioMart in Ensembl Plants. If you are completely new to BioMart have a look at our latest video and tutorials. If you want to convert the coordinates of these IDs from one assembly to another in V vinifera, give our assembly converter a try.

ADD COMMENTlink written 3.5 years ago by Denise - Open Targets5.0k
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