Hi Suman, Unfortunately, GFF3 files are not supported as custom tracks for the genome browser. We recommend converting your GFF3 file to a bed (more information can be found here: http://genome.ucsc.edu/FAQ/FAQformat.html#format1). Once you have converted it you can use the bedItemOverlapCount utility (http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads in "Other executable binary utilities") to build a bedGraph, which will allow you to see the peaks.
Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 9/1/10 7:16 AM, suman pal wrote: > Dear Sir/madam, > > I am postdoctoral fellow working in CCMB, Hyderabad,India in the laboratory > of Functional Genomics and Gene Silencing Group. > > I will be highly obliged if you kindly suggest me some steps to display my > gff3 Nimblegen ChIP on Chip genome tiling array files in the UCSC genome > Browser.The organisms is Drosophila Melanogaster (dm3 rel5). > > When I am adding the gff3 files in custom track the track is looking inverted > to me. Is there any way to change this view. > > Most importantly Is there any way I can display the peak scores or log2 > ratios as well. > > > Looking forward to your reply. > > Sincerely, > Suman Pal, > Laboratory for Gene Silencing and Functional Genomics > G-110, South wing, ground floor, > CCMB,Hyderabad,India > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
