Good Morning Vaibhav: To calculate GC percent over regions greater than 5 bases, you need to use the kent source tree program: hgGcPercent
Fetch the kent source tree and build this program. You can then calculate any window size GC percent from the .2bit file. The program is in the directory: src/hg/makeDb/hgGcPercent/ See also: http://genomewiki.ucsc.edu/index.php/Wiggle --Hiram vaibhav jain wrote: > Hello everyone, > I want to download the GC percent of Rat genome, when I am trying from > Table browser I am getting data in 5 bp window and that too only of one > chromosome at a time. Now I want the GC percent in much higher window > atleast 1 kb, so is there any tool (in UCSC/Galaxy) through which I can get > the data in 1 kb or higher window . Also when I downloaded the data from > download page then I could not see any kind of percentage or I am not able > to interpret the data in proper manner. This how the file looks, some of the > starting lines of the files are: > > 585 chr1 0 5120 chr1.0 5 1024 0 /gbdb/rn4/wib/gc5Base.wib 0 100 781 32475 > 1671220 > 585 chr1 5120 10240 chr1.1 5 1024 1024 /gbdb/rn4/wib/gc5Base.wib 0 100 1009 > 33205 1516480 ... > 589 chr1 525310 530430 chr1.99 5 1024 98233 /gbdb/rn4/wib/gc5Base.wib 0 100 > 1024 41420 2149200 > > Thanks and regards > Vaibhav Jain > Research Scholar @IGIB > New Delhi, INDIA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
