Hi Rita, There is not a way to convert formats using the Genome Browser directly, but you could convert formats using a script. There is an example script in our genomewiki, here:
http://genomewiki.ucsc.edu/index.php/Wiggle_BED_to_variableStep_format_conversion -- Brooke Rhead UCSC Genome Bioinformatics Group On 2/6/12 10:34 AM, Rita Rebollo wrote: > Hello, > > I am trying to use a tool called SitePro within Cistrome. This tool uses WIG and BED files to compute score profile on the BED regions. I have downloaded, through Cistrome/Galaxy the Encode wig files (in cistrome that's : get data => UCSC main => expression and regulation, LICR TFBS, signal file (WIG file) => send to galaxy. This is how the file looks like : > > track type=wiggle_0 name="ES-Bruce4 H3K4me1" description="ES-Bruce4 H3K4me1 > Histone Modifications by ChIP-seq Signal from ENCODE/LICR" > chr1 3002700 3002800 0.17 > chr1 3002800 3002900 0.17 > chr1 3002900 3003000 0.17 > chr1 3004200 3004300 0.13 > chr1 3010800 3010900 0.13 > chr1 3011000 3011100 0.17 > chr1 3011100 3011200 0.13 > chr1 3016200 3016300 0.17 > chr1 3016300 3016400 0.17 > ... > > As you can see this WIG file has a bed-like structure, which is NOT accepted by SitePro (from the sitepro developers : "The problem is we only support 'variableStep' of wig files. If ENCODE wig file is fixStep or bed-like format, SitePro may fail."). > > Is there a way the UCSC could format the WIG files as variablestep and not > bed-like? > Is there a way a could convert these bed-like WIG files into variablestep? > > Thank you for your help, > > > Rita Rebollo, PhD > Post doctoral fellow in Dixie Mager's lab > Terry fox lab, BCCRC - Vancouver CANADA > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
