question about TSS

[Lijing Yao]

Hi

    I have a question about the TSS file. I want to find the TSS of a list of gene. I have the gene name such as STAT6. And I go through the file of switchDbTss.txt, there is no such kind of name on it instead, they have names like chr1_P00M. I wonder if there is file that can connect the two name to each other?

Thank you for your help.

Lijing 

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Lijing yao
Dept. of Biochemistry & Molecular Biology
USC/Norris Comprehensive Cancer Center
1450 Biggy Street, NRT 6514
Los Angeles, CA 90033
Phone: (213) 344-6916

email: liji...@usc.edu

[Pauline Fujita]

Hello Lijing,

We recommend using the transcription start sites annotated in the UCSC
genes track. You can read more about this track on the track
description page here:

http://www.genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene

You can get the transcription start sites for a list of genes using
our Table Browser here:

http://www.genome.ucsc.edu/cgi-bin/hgTables

Once there you will need to filter for your list of gene names from a
secondary table. Do this by selecting:

clade: Mammal
genome: Human
assembly: hg19
group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: knownGene
region: genome

then click "create" filter and in the "hg19.kgXref based filters"
section you can enter your gene names - in the "geneSymbol does match"
field as a comma separated list - like so:

DDX11L1, DDX11L9, DQ597235, STAT6

and click "submit". Then in the main Table Browser menu select:

output format: "selected fields from primary and related tables"

and click "get output". Then in the next menu, from the "Select Fields
from hg19.knownGene " section select "txStart" to get the
transcription start sites.

If you have further questions please feel free to contact the mailing
list again at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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