Hello, Is there any way to create 2 coverage tracks from Chip on Chip data (BED format files) one per strand e.g. one for the "Positive strand" and the other from the " Negative strand" in the UCSC browser.
Can the merge Bedgraph tools be used assigning negative values to the chrom coordinates in the negative strand? Also how to assign separate colors to them. Sincerely Suman. --- On Thu, 9/16/10, Hiram Clawson <[email protected]> wrote: > From: Hiram Clawson <[email protected]> > Subject: Re: [Genome] conversion of Bedfile to BedGraph problem > To: "suman pal" <[email protected]> > Cc: [email protected] > Date: Thursday, September 16, 2010, 12:08 AM > Good Morning: > > The example you list here is already a bedGraph file. > Please note > the description of this file format and how to use it in a > custom track: > http://genome.ucsc.edu/goldenPath/help/bedgraph.html > > --Hiram > > suman pal wrote: > > Hello, > > > > I think the Windows environment of my PC is not > allowing the program to download bedItemOverlapCount > properly from the UCSC site. Thus it cannot run the file in > the Windows environment. Is there any way I can bypass the > file problem using some command prompts. > > > > Alternatively, if I just add the following lines in > the text editor of the bed file and directly upload as > custom track will it work ! e.g. > > > > #sort bedFile.bed | bedItemOverlapCount [options] > <dm3> stdin > > browser position chr4:0-7164 > > chr4 0 > 245 3.39 > > chr4 690 > 1230 3.14 > > chr4 713 > 1258 3.31 > > chr4 1575 > 2130 2.84 > > chr4 1932 > 3506 3.39 > > chr4 2310 > 2645 3.21 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
