3'UTR Strip from all genes
0
0
Entering edit mode
3.9 years ago
josolvason • 0

Hi,

I am interested in stripping the sequences of 3'UTRs of all genes from the UCSC genome browser. So far I've been toying around with cruzdb. Its simple enough to do with the genome browser GUI (browser -> search gene -> knownGene -> genomic sequence -> click only 3' UTR -> sequence.fasta). I assume since I can filter using a GUI I can also code this into python through an API? Not necessarily looking for an answer here, but direction would be greatly appreciated. Also, I'm keen on avoiding abuse of the ucsc server. Go Slugs!

Thanks,

Joe

genome python ucsc utr mysql • 1.2k views
ADD COMMENT
0
Entering edit mode

It should be possible to do using mysql and right queries at UCSC or by using BioMart at Ensembl via API or R.

ADD REPLY

Login before adding your answer.

Traffic: 2441 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