NGS data

[Caroline-17]

Hi,

I'm trying out GBrowse2 to visualise some ChIPseq short read data. Our
collaborators want to be able to look at the individual short reads
(which after filtering is about 13mill ChIP reads and 11mill Input
reads). According to a previous thread
(http://www.nabble.com/NGS-in-GGB-td22477878.html): "with GBrowse2,
incorporating nextgen data should be fairly easy." Can anyone elaborate
on this? Should I be using wig files? If so, can I divvy up the original
file into small chunks and make separate binary wig and gff files for
each one? Will a MySQL database loaded with bp_seqfeature_load.pl cope
with 13 million features  or will it grind to a halt?

Thanks!
Cass

--
Dr. Caroline Johnston

0207 848 5306

James Black Centre
Centre for the Cellular Basis of Behaviour
Department of Neuroscience
Institute of Psychiatry
Kings College London
125 Coldharbour Lane
London SE5 9NU

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[Dave Clements, GMOD Help Desk]

Hi Caroline,

The technology that Scott mentions at the end of that thread is the
Bio-SamTools database adaptor for GBrowse.  This is available in its
current alpha state in the GMOD SourceForge CVS directory under the
gbrowse-adaptors project.  SAMtools is a set of programs and file
formats for representing short read data in a platform agnostic,
indexed, and compressed format.  See samtools.sourceforge.net for more
on that.

Unfortunately, there is currently very little documentation on this.
However, I'll be presenting this at a couple meetings in the coming
weeks, and once that happens, I'll upload the presentations to the
wiki.  After that, and hopefully before the end of June, there will be
detailed documentation on this on the GMOD web site.  We have seen a
lot of interest in this lately.

I have shown short read data with both a SeqFeatureStore backend and a
SAMtools backend.  For summary data ("wiggle" data), I think they are
roughly comparable.  However, the SAMtools backend appears to be much
faster, and is much more compact.

Dave C

On Mon, Jun 1, 2009 at 9:28 AM, Caroline <Caroline.E.Johnston@...> wrote:

> Hi,
>
> I'm trying out GBrowse2 to visualise some ChIPseq short read data. Our
> collaborators want to be able to look at the individual short reads
> (which after filtering is about 13mill ChIP reads and 11mill Input
> reads). According to a previous thread
> (http://www.nabble.com/NGS-in-GGB-td22477878.html): "with GBrowse2,
> incorporating nextgen data should be fairly easy." Can anyone elaborate
> on this? Should I be using wig files? If so, can I divvy up the original
> file into small chunks and make separate binary wig and gff files for
> each one? Will a MySQL database loaded with bp_seqfeature_load.pl cope
> with 13 million features  or will it grind to a halt?
>
> Thanks!
> Cass
>
> --
> Dr. Caroline Johnston
>
> 0207 848 5306
>
> James Black Centre
> Centre for the Cellular Basis of Behaviour
> Department of Neuroscience
> Institute of Psychiatry
> Kings College London
> 125 Coldharbour Lane
> London SE5 9NU
>
> *** Please note new email address ***
>
>
>
> ------------------------------------------------------------------------------
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> is a gathering of tech-side developers & brand creativity professionals. Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, &
> iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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Learn more about GMOD at:
  SMBE: http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
  Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
  AGA Next Gen Seq in Non-Models: http://www.regonline.com/Nextgeneration

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