Hello Suman, Are you talking about creating two custom tracks from tracks from your own data? Or from existing tracks in the Genome Browser?
If you want to create two custom tracks from your own data, separate the positive and negative strand data into two files, and then upload them separately via the custom tracks tool (http://genome.ucsc.edu/cgi-bin/hgCustom). If you want to create two custom tracks from an existing Genome Browser track, select it in the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), add a filter so that "strand does match +" or "strand does match -", and choose custom track as the output format. > Can the merge Bedgraph tools be used assigning negative values to the > chrom coordinates in the negative strand? I am not sure which tools you are referring to, but chromosome coordinates with negative values will not display in the Genome Browser. If you want to color your track items according to strand, you can use the "colorByStrand" track line attribute described here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK If you need more tools for manipulating your data files, you might find the Galaxy website helpful: http://main.g2.bx.psu.edu/ (Galaxy's helpdesk address is [email protected]). I hope this helps. If you need more help with the UCSC Genome Browser, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 09/20/10 09:19, suman pal wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
