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How to obtain data on the coordinates of the Exon region from UCSC

I would like to download the coordinates of the exon region in the Hg19 region from UCSC, but I don't know which link is the right one.

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.ensGene.gtf.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.knownGene.gtf.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.ncbiRefSeq.gtf.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.refGene.gtf.gz

Which of these links would be appropriate? I would appreciate it if you could tell me.

hg19 ucsc exon
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written by ayasu • ayasu

these are gene definition of different databases. Look at the definition and choose the one you need. Most exons should be ubiquitous in all files.

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

UCSC is accessible via MySQL (https://genome.ucsc.edu/goldenPath/help/mysql.html) and I've always found it very useful to browse tables this way to see exactly what is contained in a specific table within a specific database. I use Sequel Pro on Mac and it's very convenient. Screenshot below of hg19 database, knownGene table.

SequelPro_UCSC

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written by noodle noodle

Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to the photos. Thank you.

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written by ayasu • ayasu

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