Working With Phastcons Files
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8.2 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 • 2.7k views
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8.2 years ago
KCC ★ 4.0k

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.

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8.2 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.

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

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