Discrepancies in conservation scores for D.Melanogaster(dm6)

[Alara Erenel]

Dear Authorized Personnel,

I hope this mail finds you well. I am Alara ERENEL, a second-year PhD student at Oxford Brookes University. I am trying to retrieve phyloP27way and phastCons27way scores of D. Melanogaster(dm6) from the UCSC genome browser to use it with my ChIP-Seq data locally - with IGV. However, when I downloaded the bigwig files from the appropriate links (for phyloP27Way: http://hgdownload.soe.ucsc.edu/goldenPath/dm6/phyloP124way/dm6.phyloP124way.bw and for phastCons27way: http://hgdownload.soe.ucsc.edu/goldenPath/dm6/phastCons124way/dm6.phastCons124way.bw) the scores shown on IGV are not the same with scores shown on UCSC genome browser for the same location. Both are aligned to dm6 so it shouldn't be the reason. I tried to convert wigfix files to bed with BEDOPS, but those files were not working either. Can you please help me with the issue?

I am looking forward to your reply and help. Have a nice day and cheers from Oxford!

Kind Regards,

Alara

Alara ERENEL, B.Sc., M.Sc.

Ph.D. Research Student

Department of Biological and Medical Sciences

Faculty of Health and Life Sciences

Oxford Brookes University

Gipsy Lane Oxford, OX3 0BP, UK

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

The discrepancy you are seeing is due to a lossy compression that the Genome Browser uses to display wiggle data. For this reason, we provide the original scores to download. More information about this can be found in the following FAQ entry:

https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloadConservation

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.

Jairo Navarro
UCSC Genome Browser

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