How to obtain data on the coordinates of the Exon region from UCSC
1
0
Entering edit mode
3 months ago
ayasu • 0

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 • 586 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
3
Entering edit mode
3 months ago
joe ▴ 430

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

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1536 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6