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
