[Biopython] How to get sequences upstream of TSS of genes?

[Steve Lianoglou]

Hi,

On Oct 16, 2009, at 11:44 AM, Peng Yu wrote:

> My question was how to figure what type of geneID it was for 'Krt83'?
> I tried 'Ensembl Gene ID(s)' in the menu and put 'Krt83' in the box
> below it. But I get an empty mart_export.txt file.


I'm guessing you're filters are set wrong.

Try with:
  * FILTER set to: MGI symbol
  * ATTRIBUTES set to: Ensembl Gene ID, Ensembl Transcript ID, MGI  
Symbol

You'd get:

Ensembl Gene ID	Ensembl Transcript ID	MGI symbol
ENSMUSG00000047641	ENSMUST00000108897	Krt83
ENSMUSG00000047641	ENSMUST00000081945	Krt83

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact