Hi all,
I am a new user to Galaxy. Recently I uploaded a bed file to Galaxy and then converted it to hg18 format in order to run a phastCons scoring on it. The fields returned were all NaN, though. I then converted the hg18 format to hg17 in order to see if that would make a difference, but it still returned NaN each time. At this point, in order to test if it was simply my data that had a problem, I found and viewed a specific region in the UCSC genome browser to verify that it did, in fact, include regions with conservation, I entered that sequence into Galaxy in bed format and attempted to get phastCons scores for it, but still received NaN for the results. At this point, I have no idea what is going on. I believe that this must be a bug, since I am fairly certain that my bed files are in the correct format.
All of these were run on the main Galaxy server on and off during the past week. If anyone could help me figure out what is wrong, I would appreciate it very much.
Thanks, Diana