Conversation score by bigWigAverageOverBed

[Maryam Labaf]

Hi,

I did run the motif analysis by HOMER for Drosophila. I performed the motif conservation analysis using bigWigAverageOverBed utility under the dm6.27way.phastCons.bw bigwig files. My command line is:

bigWigAverageOverBed  dm6.27way.phastCons.bw  HOMER_motif.bed -minMax out.bed

So, I have two questions, first want to make sure about using this utility to get the conversation score. And my second question is related in how can I use MafFilter utility to filter out blocks that don’t have a wanted assembly.

Thank you for your help,

Best,

Maryam Labaf,

Graduate student,

University of Massachusetts Boston.

[Matthew Speir]

Hi, Maryam. 

Thank you for your question about bigWigAverageOverBed. I apologize for the delay in our response. 

The bigWigAverageOverBed tool will average the score in a bigWig over regions specified in the BED file. If all you care about is a single score for each region that seems reasonable. You may be aware already, but we also provide PhastCons scores for a 124-way alignment between dm6 and 123 other insect genomes: http://hgdownload.soe.ucsc.edu/goldenPath/dm6/phastCons124way/

Can you clarify your question about mafFilter a little bit? The PhastCons scores are calculated over the entire 27-way alignment. If you remove MAF blocks from the alignment after the score has already been calculated, then the score does not change. If you wanted a conservation score based only on the filtered species, then you would need to recalculate the PhastCons scores on the new, filtered MAF file. 

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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