Hello, Amit. Unfortunately, there is no way to include the gene name in the Table Browser output when selecting BED as your output format. There is a way to obtain the gene names associated with your Ensembl identifiers, though. You will need to perform a second Table Browser query. Perform the following steps:
1. Perform your query as before, but instead of BED, change your output format to "selected fields from primary and related tables" 2. Click the "get output" button 3. In the "Linked Tables" section at the bottom of the page, check the "hg19.ensemblToGeneName" checkbox 4. Click the "Allow Selection From Checked Tables" button 5. In the "Select Fields from hg19.ensGene" section, check the "name" checkbox 6. In the "hg19.ensemblToGeneName fields" section, check the "value" checkbox 7. Click the "get output" button Please note that while this will match the gene name with your Ensembl identifiers, you will still need to compare your two lists manually. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Amit Pande Sent: Monday, April 16, 2012 9:02 AM To: [email protected] Subject: [Genome] regarding Ensembl annotation Hi, I want to analyze 1kbps upstream regions of the protein coding genes for promoters. I am experiencing difficulties: 1. The associated "transcripts" do not have gene names associated with them in the table browser . This is how I tried to extract these regions : from the gene prediction track "output format" BED. 2. then it asks " Create one BED record per: Upstream by bases 3. this is what I get : chr1 67163158 67164158 ENST00000371026_up_1000_chr1_67163159_r 0 - chr1 67163055 67164055 ENST00000371023_up_1000_chr1_67163056_r 0 - chr1 67163158 67164158 ENST00000395250_up_1000_chr1_67163159_r 0 - chr1 201325404 201326404 ENST00000309502_up_1000_chr1_201325405_f I want the gene name with the associated transcript for further analysis..... Can you please help. regards, Amit _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
