Obtaining phastCons conservation score for every gene in the Human genome
2
1
Entering edit mode
6.9 years ago
jeff.ohana ▴ 10

Hey guys,

Does someone has ever calculated the averaged PhastCons conservation score for every gene of the Human genome? One averaged conservation score for every gene.

If not, How could I calculate the average conservation score for every gene since the UCSC browser gives the conservation score for each base in a gene?  Does somebody has an idea of a python code that could calculate the averaged conservation score for each gene? knowing that the genes are in a TXT file separated from each other by a sentence; and for each gene there are many conservation scores for each of their bases, I would like to abstain only one averaged conservation score for each gene.

Need to obtain an answer ASAP,

All the best,

Jeff O.

conservation score genome phastCons • 6.1k views
ADD COMMENT
5
Entering edit mode
6.9 years ago

ADD COMMENT
0
Entering edit mode
5.8 years ago
egarmo • 0

Trying to replicate the method, so far only one important variation. The url argument for wget will take ftp rather than http. As for the rest of the url, it is valid on this date of accession.

ADD COMMENT

Login before adding your answer.

Traffic: 856 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