UCSC to ENSEMBL chromosomes

[JC Grenier]

Hello there,

I'm working on a big project consisting of comparing multiple mammals transcriptomes. I'm having troubles with one of the tools I want to use to get orthologous genes between the species. The tool is using the liftover chain files. So far it was right, since I was able to find all the chain files for all the comparisons I want to make.

The problem is that the team with which we are working are using the ENSEMBL genome release. So the chromosome names are different between the genomes and the chain files, so nothing works correctly. I know that normally I should just remove the "chr" in front of the chromosome name, but, the alternative haplotypes are giving me headaches.

I was able to get for some of my genomes a conversion files, which was taken from a sql database on your ftp server.

Here's an example of command line that I used to get it for the Human for example :

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e "select * from ucscToEnsembl;" hg38 > hg38.conversion

That is working well!

I'm still missing those genomes :

bosTau8
oviAri3
rheMac8
rn6
susScr3
susScr11

Thanks a lot for your help!

Jean-Christophe Grenier

[Robert Kuhn]

Hello, Jean-Christophe,

We recently released conversion tables for many genomes.  The table,

chromAlias in the respective databases should be able to help you

convert chrom names.  Beyond the contents of those tables, I'm afraid

we are unable to help further.

best regards,

     --b0b kuhn

     ucsc genome bioinformatics group

share the Browser with colleagues.  host a workshop: http://bit.ly/ucscTraining 

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[JC Grenier]

That's awesome. It seems to have everything I need.

Thanks a lot Robert.

JC

2018-03-27 17:32 GMT-04:00 Robert Kuhn <ku...@soe.ucsc.edu>:

Hello, Jean-Christophe,

We recently released conversion tables for many genomes.  The table,

chromAlias in the respective databases should be able to help you

convert chrom names.  Beyond the contents of those tables, I'm afraid

we are unable to help further.

best regards,

     --b0b kuhn

     ucsc genome bioinformatics group

share the Browser with colleagues.  host a workshop: http://bit.ly/ucscTraining 

--

-- 

Jean-Christophe Grenier, M.Sc.
 
-----------------------------------------
Bio-informaticien

Laboratoire de Luis Barreiro

CHU Sainte-Justine

3175, Côte Sainte-Catherine, local 17.6.028

Tél : 514-345-4931 poste 7605

-----------------------------------------

[JC Grenier]

Hello Robert,

I have another question concerning the baboon reference.

There's multiple liftOver files from hg38 to papAnu reference genome. Can you tell me to which reference genome

hg38ToPapAnu4.over.chain refers to?

Which one corresponds to the actual latest release on Ensembl?

Thanks a lot for your help.

JC

[Hiram Clawson]

Good Afternoon JC:

The UCSC database papAnu4 corresponds to the Ensembl release Papio_anubis.Panu_3.0
UCSC has an extra sequence for mitochondrial chrM.

papAnu3 is equivalent to Ensembl release Papio_anubis.PapAnu2.0

--Hiram

>> *Bio-informaticien*
>> *Laboratoire de Luis Barreiro*
>> *CHU Sainte-Justine*

>> 3175, Côte Sainte-Catherine, local 17.6.028

>> *Tél : 514-345-4931 <514-345-4931> poste 7605*
>> -----------------------------------------
>>
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