Thanks Julian, for you feedback, I will keep your feature request in my
mind, and will think about implementing something like different
modes/types in geom_alignment or stat_mismatch function in ggbio.

Tengfei

On Thu, Feb 28, 2013 at 2:31 PM, Julian Gehring <julian.gehring@gmail.com>wrote:

> Hi Tengfei,
>
> What you describe covers what I tried to do so far (overlapping tracks,
> really a hacky task).  Having these modes would be very handy to have,
> especially in combination with the other capabilities of 'ggbio'.  All the
> three modes would be good to have; I would consider (1) the most useful one
> for me at the moment.  The more detail to incorporate in the alignments
> (e.g. including SNV information of a VCF file) would need additional
> relations between BAM alignments and the VCF.
>
> I am not aware of any R package with this functionality, but I see a large
> potential for this.  Currently, I interact with IGV using batch mode, but
> this far away from being a good and long-term solution.
>
> Best wishes
> 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  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...
>>
>> 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
>>
>>


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

	[[alternative HTML version deleted]]

