[Genome] Rat Ensembl genes and QTLs

[Archana Thakkapallayil]

Hello Rick,

This task can be accomplished with the Table Browser intersection tool.

Click the "Tables" link at the top of the page and follow these steps:

1. Select the genome and assembly of interest and then choose 'group: 
Genes and Gene Prediction Tracks', 'track: Ensembl Genes', and 'table: 
ensGene'.

2. Select "genome" as the region.

3. Click on the "paste list" or "upload list" button to add the list of 
Ensembl gene ids. You need to have a list of your Ensembl gene ids in a 
consistent format that the Table Browser can use (one ID per line).

4. Select custom track as the output and press the "get output" button. 
Then hit "get custom track in table browser" button. This creates a 
track in the Table Browser that represents the Ensembl genes that you 
have uploaded.

5. Then you can create an intersection of these genes with the RGD QTL 
track. To do this make the following selections:

  group: Mapping and Sequencing Tracks
  track: RGD QTL
  table: rgdQtl
  region: genome

  Press the "intersection: create" button and on the intersection page 
choose 'Custom Tracks' as the group name, and the custom track and table 
name. Then select the radio button 'All RGD QTL records that have any 
overlap with tb_ensGene' and hit "submit".

6. Output the intersection as BED or custom track. This gives you the 
list of all QTL's that overlaps with your Ensembl gene list.

I hope that this helps you. Please let us know if you have further 
questions.

Regards,

Archana
UCSC Genome Bioinformatics Group


Dixon, Dr R. wrote:
> Dear Genome team,
>
> I have a list of Ensembl Gene ids (hundreds) (ENSG....) - I would like
> to obtain the QTLs that overlap with these genes... How do I do this
> with the ucsc browser table structre
>
> Thankyou
>
> Rick
>
>
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