Hi Peng, Negative values can be displayed in wiggle tracks. For instance, see the "Basewise Conservation (phyloP)" subtrack that is part of the Conservation track on the hg19 assembly. It has a default vertical viewing range of -0.3 to 2.
Does the track you are looking at definitely have negative values in the region you are examining? Also, make sure you have selected the "Data view scaling: use vertical viewing range setting" option. Regarding your original question, one of our engineers offered an outline of how you could create a third wiggle file that is the difference of two wiggles: --- A manual procedure could be done, but it would require some extremely large files: 1. extract the data for each track and turn them into values for single bases in a two column sorted format: chr_position value 2. run the unix join function on the two files on the 'chr_position' column, to produce a third file: chr_position value1 value2 3. Run awk on that file to calculate value1-value2 or whatever sum function and get it back to bedGraph format: chr position position+1 sumValue 4. now bedGraphToBigWig --- The last step would get your data into bigWig format, described here: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 It could then be used as a custom track. -- Brooke Rhead UCSC Genome Bioinformatics Group On 06/27/11 12:14, Peng Yu wrote: > Hi Brooke, > > It seems that the browser can not display negative values, right? Even > I set "Vertical viewing range" to a negative number, the browser > doesn't seem to display anything less than zero. Is it the case? > > > On Mon, Jun 27, 2011 at 1:46 PM, Brooke Rhead <[email protected]> wrote: >> Hi Peng, >> >> No, there is not an option to display the difference between two wiggles in >> the Genome Browser. You could subtract the two wiggles yourself and then >> load a the resulting wiggle as a custom track, though. >> >> -- >> Brooke Rhead >> UCSC Genome Boioinformatics Group >> >> Peng Yu wrote on 6/25/11 7:29 AM: >>> Hi, >>> >>> I know that this may not be possible, but I just want to double check >>> to make sure. Suppose I have two wig files, A and B, is there a way to >>> display A-B in genome browser? >>> > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
