weighted read display - genome browser

[svm]

Hi,
does anyone know of a genome browser that collapse all exact reads to one read, but with a thickness or color that can reflect the number of reads for that loaction?
in other words if i have a genomic location say 1-50 that has 200 reads and another location with 3-75 with 20 reads, i would like to see a longline for 1-50 location with a very thickline (or an appropriate color), while 3-75 gets a much smaller thickness? Can UCSC do this? anyother favorites you know for bed file visulaization witht this purpose?

something like
___________________________
___________________________
___________________________ for 1-50


___________________________________ for 3-75

thanks
svm

[Jim Robinson]

Hi, its an interesting idea but might be difficult in practice. Would you distinguish between 10 reads, 100 reads, and 1000 reads?

Jim

[svm]

yes Jim, anything approximate would be fine..like you are implying one could be on a log-scale for instance... the scale can be given to the browser in a bed file, the browser just needs to collapse and weight the "number of reads" given to it (the number could be log of the actual reads) .. i am happy to play around with the scale, i just need a browser with that feature.

[Jim Robinson]

Hi, can you expound on what new information you would glean from such a view that you don't already get in a coverage plot? There is a little extra information there, but is not clear what would be important.

Also, how do you define an identical read, same bases or just same position?

[gringer]

Would wiggle plots be appropriate for your uses? They are at least supported by GBrowse (and likely other programs):

http://genome.ucsc.edu/goldenPath/help/wiggle.html

Here's an example of GBrowse use, where the density is used to change the colour (rather than the thickness) of the line:

http://gmod.org/wiki/GBrowse/Uploading_Wiggle_Tracks