Working With Phastcons Files
2
0
Entering edit mode
11.5 years ago

Hi I wanted to identify whether the regions that i have (BED format, mouse mm10) are conserved. I am downloading mm10.60way.phastCons60wayEuarchontoGlire.bw file from ucsc (bigwig file). is there any easy way that i can get the average score for my intervals? how about using Galaxy server? I have also come across with few programs in Biostar for the same but couldnt figure out how to use them for my purpose

galaxy • 3.6k views
ADD COMMENT
1
Entering edit mode
11.5 years ago
KCC ★ 4.1k

I think you should use the bigWigAverageOverBed command which can be found here

The usage is:

bigWigAverageOverBed in.bw in.bed out.tab

You can find more information here.

ADD COMMENT
0
Entering edit mode
11.5 years ago
polarise ▴ 380

My solution was to put the data in an SQLite database. I don't know if that's the most efficient but I was able to speed up the time to get scores for disjoint sites.

ADD COMMENT
0
Entering edit mode

could you please explain me properly i am not able to get it

ADD REPLY

Login before adding your answer.

Traffic: 1493 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