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Working With Phastcons Files

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
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updated by Biostar Biostar • written by ancient_learner ancient_learner

2 answers

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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updated by Ram Ram • written by KCC KCC

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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written by polarise polarise

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

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written by ancient_learner ancient_learner

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