Hello again, I should clarify that this feature works as you are seeing it for bigWig tracks but has abbreviated output (as you've noticed). If you are comfortable running command line applications you may be interested in grabbing our source code and running the "bigWigSummary" or "bigWigAverageOverBed" programs. The bigWigAverageOverBed would be easier if all you need are averages within the region. If you want other stats you would have to execute bigWigSummary in a script, once for each of your regions, with the dataPoints parameter set to 1, and the type option set to the statistic you want.
You can read more about obtaining our source code here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads Depending on what system you are using you will likely find the relevant applications here: http://hgdownload.cse.ucsc.edu/admin/exe/ Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 2/17/12 2:36 PM, Pauline Fujita wrote: > Hello Nicholas, > > Unfortunately the tracks you are looking at are based on bigWig format > files (vs. wig files) and the summary/statistics feature is not > currently available for these tracks in the Table Browser. We are > currently looking into adding this functionality for these tracks. > > Best regards, > > Pauline Fujita > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > On 2/14/12 8:10 AM, Nicholas Light wrote: >> Hi, >> >> I have been using summary/statistics feature of the table browser (hg18) >> with a list of defined coordinates, using ENCODE tracks e.g >> (wgEncodeBroadChipSeqSignalGm12878H3k4me3), to obtain a table of summary >> statistics for each list of coordinates I provide. However now using >> summary/statistics in the table browser (except now hg19, instead of hg18), >> for the same tracks, I obtain only a short summary report for the entire >> data range, rather than a table with rows for each pair of coordinates. Is >> there a way to get the full table view to appear in the summary/statistics >> using the hg19 assembly? >> >> Thanks, >> >> Nicholas Light >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
