[Gmod-ajax] Wiggle Tracks in JBrowse

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[Gmod-ajax] Wiggle Tracks in JBrowse

Andrew Shinohara
Hello,
     I am generating a wiggle track for the human genome using 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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Re: Wiggle Tracks in JBrowse

Ian Holmes
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
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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