Re: [Gmod-ajax] Wiggle Tracks in JBrowse

[Ian H. <ih...@be...>]

Hi Andrew,

The logarithmic nature of zoomlevels means that the disk usage is 
dominated by the highest zoomlevel (one base per pixel). So changing the 
number of pre-rendered zoomlevels won't help too much.

For a ~3.2 gigabase genome, it does not seem totally out of whack for an 
image track (such as a wiggle track) to require 10 gigabytes of storage. 
That's about 3 bytes/base. I would expect of order 2 bytes/base (the 
highest zoomlevel you expect ~1 byte/base; the factor of 2 is about what 
you get from the geometric series corresponding to the sum over 
zoomlevels).  A bit more due to filesystem cruft.

So 3 bytes/base is not too bad... *if* the wiggle plot is purely random. 
If it's nonrandom, e.g. if it contains big swathes of nothing, then it 
should be possible to compress it much better than that - although we 
haven't really played with the compression too much.

Bottom line is that if you need basepair-resolution pre-rendered 
graphics (which is how JBrowse handles wiggle tracks) on a gigabase 
genome, you're going to need gigabytes of storage for each track...

best wishes
Ian


Andrew Shinohara wrote:
> Hello,
>      I am generating a wiggle track for the human genome using 
> wig-to-json.pl <http://wig-to-json.pl>.  I am finding that for 1 wiggle 
> track for the human genome, it is producing about 10GB of images.  I was 
> wondering if there is any way to reduce the number/size of images 
> generated for each track?  Is it possible to give a minimum and maximum 
> zoom level so that less images are generated or something along those lines?
> 
> Thanks,
> Andrew
> 
> 
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