Exon Bed File for Chromosome

[Summaira Yasmeen]

​Hi,

​​We are working on the non-coding part pf human DNA in order to get rid of exons we are looking for whole chromosome bed file of exons. Through table tool we're unable to fetch the required bed file. Can you please guide us.

Please answer ASAP

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​Thanks, ​

Summaira Yasmeen

M. Phil Scholar,

​Comparative Evolutionary Genomics Lab, ​

National Center for Bioinformatics (NCB)

Quaid-I-Azam University Islamabad,Pakistan

[Christopher Lee]

Hi Summaira,

Thank you for your question about obtaining a bed file of exon positions for a human chromosome. We can use the table browser to create this file:

1. Head over to the table browser http://genome.ucsc.edu/cgi-bin/hgTables
2. Select "Mammal", "Human" and "Dec. 2013 GRCh38/hg38" from the "clade", "genome" and "assembly" dropdowns
3. Select "Genes and Gene Predictions", "GENCODE v22" and "knownGene" from the "group", "track" and "table" dropdowns
4. For "region" choose "position" and then enter your chromosome of interest into the search box
5. In the "output format" dropdown select "BED - browser extensible data"
6. Enter a name for your bed file in the "output file" text box
7. Click "get output"
8. Enter a custom track header if you would like to later view this data in the browser

9. To include all exons in your output (including non-coding exons), choose the "Exons plus" button. To include coding exons only, select "Coding Exons". To include non-coding exons only, select either "5' UTR Exons" or "3' UTR exons" (you will have to perform two separate queries to get both).

10. Now select "get BED" to download your bed file of exon positions, one per line.

For more information on the table browser please see the Table Browser User's Guide at: https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. You can also search our archived mailing list at https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome to see similar questions that have been asked previously.

Thank you again for your inquiry and using the UCSC Genome Browser.
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
forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

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