Genomic Co-ordinates

[Apoorva Kulkarni]

Hi,

I wanted genomic co-ordinates for a list of genes which I got successfully. I need to create a BED file using these co-ordinates so when I try to save the results,it saves it as txt file but I do not see co-ordinates.The file is an HTMl file(attached for reference)

Can you please tell me how can I save the results in a proper format and use them for BED file creation.

Thank you.

Regards,

Apoorva

[Matthew Speir]

Hi Apoorva,

Thank you for your question about obtaining BED coordinates from the UCSC Genome Browser.

If you are new to using the UCSC Genome Browser, I would highly recommend that you take advantage of the training material that we provide: http://genome-euro.ucsc.edu/training/index.html. In particular, I would start with the OpenHelix videos: http://www.openhelix.com/ucsc.

Coordinates for items in a track can be obtained in BED format from the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables. For example, you could use these steps to get a set of BED coordinates for a list of genes in the GENCODE Genes v24 track for the hg38/GRCh38 human assembly:

1. Navigate to the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables.
2. Select your genome and assembly. In this example, I will be using the hg38 assembly of the human genome:
    clade: Mammal
    genome: Human
    assembly: Dec. 2013 (GRCh38/hg38)

3. Select your track and output format. In this example, I'm using the GENCODE v24 track:
    group: Genes and Gene Predictions Tracks
    track: GENCODE v24
    table: knownGene
    output: BED - browser extensible data
    output file: enter a file name to save your results to a file, or leave blank to display results in your browser

4. Next to "identifiers", click "paste list" or "upload list".
5. This step will change depending on whether you clicked "paste list" or "upload list":
    a. If you clicked "paste list" copy and paste your list of gene names into the box. Click "submit".
    b. If you clicked "upload list", click "choose file" and select the file containing you list of gene names. Click "submit".

6. Click "get output".
7. Adjust your BED output settings, then click "get BED".

If you can provide more information about the gene track you are using and some examples from your list of gene identifiers, we may be able to provide more specific information. For more information on using the Table Browser, see the User's Guide: https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

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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