Hi Libia, Just a quick note, you should use the 4th column to get the lod scores, not the 5th column. The 5th column is the BED score column, and is used to shade items (see http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED for more info). One of our engineers also had this to say:
BED score is constrained to the range 0-1000, which is not the natural range for many metrics (especially when using the BED score to shade items, when the score has to be at least 200 in order for the item to be visible). In the case of phastConsElements tables, note that the lod score has actually been tucked into the name column! (lod=18 etc) The BED score column contains a transformation of the lod score. The parameters of the score transformation are data-dependent: the median lod score is transformed to 300 and the max lod score to 1000. Not only that, but it's a log transform, not linear! Since we don't publish the transform parameters, the actual lod scores can't be recovered from the BED score column alone. But they are not so hard to parse out of the name column. (sed -e 's/lod=//'). I hope this helps! Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
