Yes you can convert a wiggle file to a bed format. The kent command line program hgWiggle can do this conversion, and the table browser in the UCSC genome browser can output this type of information. Please understand what this conversion means. This discards all the data value information, leaving only the position information of where data exists.
--Hiram varun gupta wrote: > Hi > Thanks For the reply. > I have some questions but would need to know the answer for the one i am > asking > CAN WE CONVERT A WIGGLE FILE FORMAT TO A BED FORMAT. > if yes then how > > Regards > Varun > On Wed, Jan 4, 2012 at 12:33 PM, Hiram Clawson <[email protected]> wrote: > >> Good Morning Varun: >> >> The "variableStep" data format is explained on the page you reference: >> >> http://genome.ucsc.edu/**goldenPath/help/wiggle.html<http://genome.ucsc.edu/goldenPath/help/wiggle.html> >> >> Please note the description of what wiggle data is for on this description >> page. It is for graphing data. It is not bed format and does not have >> that meaning. If you have data you need to graph, use one of these >> wiggle formats, or the more efficient bigWig format as explained on this >> page. If you have annotations you want to display on the genome, you can >> use bed format files. >> >> --Hiram >> >> varun gupta wrote: >> >>> Hi everyone >>> Thanks for your support and help >>> I have a question. I am interested in understanding the wiggle format. I >>> was going through this : >>> http://genome.ucsc.edu/**goldenPath/help/wiggle.html<http://genome.ucsc.edu/goldenPath/help/wiggle.html> >>> >>> Can you explain me what does the last paragraph means >>> >>> *Caution for sparse variableStep data* >>> *The wiggle format was designed for quickly displaying data that is quite >>> >>> dense. The variableStep format, in particular, becomes very inefficient >>> when there are only a few data points per 1,024 bases. If variableStep >>> data >>> points (i.e., chromStarts) are greater than about 100 bases apart, it is >>> advisable to use BedGraph<http://genome.ucsc.** >>> edu/goldenPath/help/bedgraph.**html<http://genome.ucsc.edu/goldenPath/help/bedgraph.html> >>> format.* >>> * >>> * >>> What do we mean by *variablestep data points* referred above. It would be >>> >>> nice if you can explain this >>> >>> Moreover can you suggest me how can we convert wiggle file into a bed file >>> >>> Thanks in advance >>> >>> Regards >>> VARUN >>> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
