Hi Hunter, > I'd like to know how to describe the Y-axis to someone.
It depends on how you generated the file, but it's probably the number of reads that cover each base in the genome. > ... can I > deduce/approximate how many reads mapped to this region with this > info (if > I know the read length)? That would require the sum of per-base coverages... you should be able to recover that from the number of bases times the average depth. For example, > *Statistics on: 284 items covering 284 bases (1.55% coverage) > Average item spans 1.00 bases. > Average value 109629 min 10.1 max 404000 *standard deviation *139315 284 bases * 109629 = 31134636 ... divide that by read length. > Illumina's peak-caller/browser allows me to > toggle the Y-axis scale between total reads, total bases, and > average base > coverage. We don't do that -- you would have to generate 3 different custom tracks, one for each measure. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 6/12/12 2:03 PM, Hunter Richards wrote: > Hi Greg, > > These came from the same track (my custom tracks). One was just a > smaller view of the same region (183 bases vs. 18.3 kb). I noticed > that if I use a BigWig I get different information when I click on the > track itself (not the control bar on the left-hand side of the > browser), compared to using a Wig file. Not sure why that is but in > both cases (see attached) I'm not sure how I can use the information > I'm seeing or if I can even derive what I'm asking about. > > I'm not sure if I'm being clear enough. Please tell me if I'm not > being clear. > > Thanks, > -hunter > > On Tue, Jun 12, 2012 at 9:52 AM, Greg Roe <[email protected] > <mailto:[email protected]>> wrote: > > Hi Hunter, > > What specific track(s) are you looking at? > > - Greg > > > On 6/11/12 1:10 PM, Hunter Richards wrote: > > When I zoom in and click on a peak in a track I get something > like this: > > *Position: *chr1:137,313,656-137,313,838 > *Total Bases in view: *183 > *Statistics on:* 183 *items covering* 183 bases (100.00% coverage) > *Average item spans* 1.00 *bases.* > *Average value* 169631 *min* 4280 *max* 404000 *standard > deviation *141420 > > > if I zoom out a bit I might see something like this: > > *Position: *chr1:137,304,597-137,322,896 > *Total Bases in view: *18,300 > *Statistics on:* 284 *items covering* 284 bases (1.55% coverage) > *Average item spans* 1.00 *bases.* > *Average value* 109629 *min* 10.1 *max* 404000 *standard > deviation *139315 > > > How can I interpret this? This is a wig track. I'd like to > know how to > describe the Y-axis to someone. This is ChIP-seq data, so, can I > deduce/approximate how many reads mapped to this region with > this info (if > I know the read length)? I know Illumina's peak-caller/browser > allows me to > toggle the Y-axis scale between total reads, total bases, and > average base > coverage. > > Thanks, > -hunter > > > > > -- > Hunter Richards > Postdoctoral Scientist > Department of Genome Dynamics > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd, Bldg 977-138 > University of California, Berkeley, 94720 > 510-486-4663 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
