Re: [Gmod-ajax] next generation sequencing visualization

[Steve T. <ste...@im...>]

Hi Mitch,

>> Yes...but we really need a decent alignment viewer at the bp level to 
>> see SNPs etc. Can GBrowse display alignments in the panel?
>>   
> 
> The volume of data is large, right?  So why would someone want to 
> eyeball it?  Won't people be running programs to identify SNPs, rather 
> than trying to do it manually?

Yes, but there will often be a need to eyeball low level data.

> 
> I worked with biologists for several years, so I know how much they like 
> to eyeball things.  But if the data volume is large, IMHO it's important 
> to push back and advocate automated analysis instead.  I'd hate to do a 
> lot of work only to find that after the initial burst of enthusiasm no 
> one used it.

> 
> Currently, there's an assumption built fairly widely into JBrowse (and 
> all other genome browsers as far as I know), which is that the 
> coordinate system defined by the reference sequence doesn't change on 
> the fly.  So it'll take a fair chunk of work to be able to show 
> insertions from resequencing.

I agree this is maybe too much to do now though it is going to be have to be thought about at some stage since there will be many 'reference' genomes. I'd be happy just to see 'simple' alignments for 
now:-).

> 
> On the other hand, if you're talking about viewing just a small region, 
> and you want to view it in alignment coordinates, and all of your data 
> is in aligment coordinates, then the JBrowse part of the work should be 
> easy to do.  We've talked about displaying per-base data (like sequence, 
> or a predicted RNA fold) in features; it's not implemented but it should 
> be straightforward to do.


As an example a popular program is called maq to align Illumina reads to a reference sequence. A useful visualization is its 'pileup' output which shows a vertical output with the reference sequence,
orientation of reads and base changes. In my experience Maqviewer doesn't seem to work on some of the systems I tried (due to some GTK issues) and reports from people that have got it working say its 
pretty basic. I run a core group and getting things running on everyone's desktops (which usually means in a browser) saves everyone's time...

In addition an alignment display would be useful for viewing conservation across species at the base pair level and is already part of the UCSC browser.

Maybe the back end could use SAM/BAM format to store the alignments http://samtools.sourceforge.net/ which appears to be a useful emerging standard. Note there is a ASCII viewer as part of the package 
which I'll check out.

Steve
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Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University