[BioC] Visualization of alignments with mismatch bases
Julian Gehring
julian.gehring at gmail.com
Thu Feb 28 23:09:49 CET 2013
Hi Tengfei,
Thanks a lot for taking this into account! I'm sure many users would
find it useful.
Do you have any code drafts on how to plot alignments and mismatches? I
know doing this will be hard, but at the moment I would be willing to
give it a try.
Best wishes
Julian
On 02/28/2013 10:05 PM, Tengfei Yin wrote:
> 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 at gmail.com <mailto:julian.gehring at 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
>
>
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