On Thu, Feb 28, 2013 at 11:08 PM, Michael Lawrence <
lawrence.michael@gene.com> wrote:

>
>
>
> On Thu, Feb 28, 2013 at 11:46 AM, Tengfei Yin <yintengfei@gmail.com>wrote:
>
>> On Thu, Feb 28, 2013 at 11:46 AM, Julian Gehring
>> <julian.gehring@gmail.com>wrote:
>>
>> > Hi,
>> >
>> > Is there a good way to visualize aligned reads with mismatch bases
>> (SNPs)
>> > along the genome (similar to what one knows from the standard genome
>> > browsers)?
>> >
>> > 'ggbio' came to my mind with which plotting a pile of reads is straight
>> > forward.  However, overlaying the mismatched bases for each reads seems
>> not
>> > that easy any more.
>> >
>>
>> Hi Julian,
>>
>> You are right, currently ggbio only supports summary of mismatch showing
>> as
>> coverage plot and barchart(?stat_mismatch), but looks like what you want
>> is
>> detailed short reads alignments visualization with mismatch bases showing
>> right on the reads, . It's possible, but not easy to do it manually...you
>> have to have two GRanges objects, one for alignment one for SNP, and plot
>> them layer by layer, the tricky part is assigning each reads fixed
>> stepping
>> level, so snp can be plotted on the right position. I will NOT recommend
>> you to do this, it's probably not worth taking time doing it. I need to
>> implement this features in some easy way.
>>
>> The tricky part is that there are different modes, 1. show reads as gray
>> rectangle, and color mismatch as segment
>
>
> Are you talking about single-read detail for #1 above or what we get from
> stat_mismatch?
>

The single-read detail, not summary mismatch from stat_mismatch(). so for
example, one 75bp reads shown as one rectangle filled with gray color, and
use vertical colored segment indicated mismatched position on this reads if
any.


>
>
>>  2. show SNP as nucleotide text,
>> A/C/T/G..,  3. show sequence detail for each alignment. those depends on
>> zoomed level and even coverage, and I guess most time you don't want to
>> see
>> bases for every reads...
>>
>>
> I think #3 is really important for any sort of diagnosis of alignment
> issues, and I would find this very useful. Right now, I'm using IGV for
> this, but ggbio would be a lot more flexible. This is probably my #1 top
> missing feature from ggbio.
>

Got it, those features are indeed important but missing, I will keep this
in mind.

I was thinking about generalize it into visualization of  DNAStringSet
first, but mismatch is not that general, require BSgenome and raw bam files
at the same time to get mismatched information. So we may extend the list
returned by scanBam(), and create a GRanges or vector with equal length of
short reads numbers for particular region which storing mismatch position
and nucleotide. I am trying to think about a more general data structure,
not only for visualization purpose, but also for command line analysis, for
example, people can simply retrieve mismatch information for any single
short read from specific data structure.

and Julian, sorry that I don't have any working example right now, I will
let you know when this feature is ready to test.

Tengfei

>
>
>
>> Just curious for future ggbio development, are those modes want you want?
>>  are you just using bam files here? no VCF files involved right? Because
>> you mentioned 'snp', I think what you mean is mismatch?
>>
>> ps:  I cannot speak for other tools, and only thing I know, in SRAdb
>> package, looks like it could fire your data in IGV..
>>
>> Thanks
>>
>> Tengfei
>>
>>
>> > Does someone of you have a good way to do this or found another solution
>> > that works for R/bioc?
>> >
>> > Best wishes
>> > Julian
>> >
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>> >
>>
>>
>>
>> --
>> Tengfei Yin
>> MCDB PhD student
>> 1620 Howe Hall, 2274,
>> Iowa State University
>> Ames, IA,50011-2274
>>
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>>
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>
>


-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274

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