Hi Frauke, If the output of your experiment is a bed file, then use the bedItemOverlapCount tool in our kent source tree (http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads in Other executable binary utilities) to create a bedGraph which can uploaded as a custom track. This mailing list answer should help you get started: https://lists.soe.ucsc.edu/pipermail/genome/2008-September/017062.html. If your output is instead a BAM file, this mailing list answer should be able to help you: https://lists.soe.ucsc.edu/pipermail/genome/2010-September/023402.html.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group ----- Original Message ----- From: "Frauke Coppieters" <[email protected]> To: [email protected] Sent: Friday, September 10, 2010 5:17:13 AM GMT -08:00 US/Canada Pacific Subject: [Genome] UCSC custom tracks - import of values for regions of interest Dear Mr./Mrs., I would like to inform whether it is possible to import custom tracks into the UCSC genome browser which represents values, such as for instance the "Conservation" track under "Comparative genomics" (hight of black bar represents degree of conservation). In particular, I would like to import the coverage of a next-generation sequencing experiment for certain genes in the Genome browser. Thank you in advance for your assistance. Best regards, Frauke Coppieters _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
