Working With Phastcons Files

Question

[ancient_learner]

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

Answer 1

[KCC]

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.

Answer 2

[polarise]

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.

[ancient_learner]

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