how to find TSS？
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Lynn Shuailiang Lin
Aug 28, 2014, 7:31:42 PM8/28/14
to gen...@soe.ucsc.edu
Dear there,
I am a graduate student in Harvard. I was wondering could you tell me how to find a gene's transcription start site or if you have a instructions, that would be great! Thanks！
Shuailiang
Matthew Speir
Aug 29, 2014, 6:26:44 PM8/29/14
to Lynn Shuailiang Lin, gen...@soe.ucsc.edu
Hi Shuailiang,
Thank your for your question about finding a gene's transcription start site. I highly recommend taking advantage of some the introductory resources that are available for the browser. I would start by watching these tutorials: http://www.openhelix.com/ucsc. You can find information on further training and tutorials here: http://genome.ucsc.edu/training.html.
The UCSC Genome Browser hosts gene predictions from numerous sources, such as RefSeq, GENCODE, AceView, Vega, and our own predictions, UCSC Genes. A full list of gene prediction tracks can be found on the track configuration page: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgTracksConfigPage=configure&hgtgroup_genes_close=0#genesGroup. You can click on the track name in the far left column for more details about what the track contains, how the predictions were produced, and more. All of these gene prediction tracks will have a txStart column that indicates the transcription start site. You can use the Table Browser to extract this txStart information from the gene track you are interest in. Please see these answers to previous mailing list questions for details about extracting TSS information from the Genome Browser:
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank your for your question about finding a gene's transcription start site. I highly recommend taking advantage of some the introductory resources that are available for the browser. I would start by watching these tutorials: http://www.openhelix.com/ucsc. You can find information on further training and tutorials here: http://genome.ucsc.edu/training.html.
The UCSC Genome Browser hosts gene predictions from numerous sources, such as RefSeq, GENCODE, AceView, Vega, and our own predictions, UCSC Genes. A full list of gene prediction tracks can be found on the track configuration page: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgTracksConfigPage=configure&hgtgroup_genes_close=0#genesGroup. You can click on the track name in the far left column for more details about what the track contains, how the predictions were produced, and more. All of these gene prediction tracks will have a txStart column that indicates the transcription start site. You can use the Table Browser to extract this txStart information from the gene track you are interest in. Please see these answers to previous mailing list questions for details about extracting TSS information from the Genome Browser:
- https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/HZqXPD6AJlo/cUYny6TLWRMJ
- https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/LxMa_yjDZk8/qfmrVzrvWu4J
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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