Hello, I cannot see your attachment (these are removed by our mail filter), however I think I know the problem even without any data.
Your BED file needs to have 5 columns of data. The 5th column is score. If you need to, just make up a "name" to pad the fourth column of data. BED format FAQ: http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1 Try this and see if it works. If you are still having problems, paste a small amount of the data (header and first few lines) into an email send directly to me (not the entire list) and I will test/troubleshoot and provide feedback, Hope this helps, Jennifer Jackson UCSC Genome Bioinformatics Group John Choy wrote: > Hi > > I'm trying to create a BED file with data from a microarray experiment. I > have 4 columns of information. Column 1=chr number, 2=start coordinate, > 3=end coordinate, 4=intensity ratio from the array. The problem I haven't > been able to solve is that the tracks which are displayed don't change > shades of gray even though I've used different values in the 4th column from > 1 to 1000. I've included the BED file I've been using as a test. Any help > would be appreciated. > > Thanks > John Choy > > NCI-Genetics Branch > Bethesda, MD 20889 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
