Hello Erik,
If the 44-way alignment has no data for some bases, it's safe to assume that there's no conservation in that region. Also note that the region of interest is in an area with repeats (You could turn on the simple repeat track in the browser to see this). I hope this is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Erik Dassi" <[email protected]> To: [email protected] Sent: Wednesday, March 11, 2009 6:54:31 AM GMT -08:00 US/Canada Pacific Subject: [Genome] hgWiggle Hi, I was trying to retrieve conservation scores for a set of regions(90k regions) by using hgWiggle. I have downloaded wib and wig files for phastCons44way track. hgWiggle is working properly, however it indicates me that no values for conservation scores exist for same bases(e.g. by typing ./hgWiggle.exe -position=chr1:142893308-142893416 phastCons44way). It is normal that no conservation scores are defined for this bases ? If it is not a problem of the software, how should I score these bases ? 0 ? thanks, erik _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
