On Thu, Feb 28, 2013 at 11:46 AM, Julian Gehring
> Is there a good way to visualize aligned reads with mismatch bases
> along the genome (similar to what one knows from the standard genome
> 'ggbio' came to my mind with which plotting a pile of reads is
> forward. However, overlaying the mismatched bases for each reads
> that easy any more.
You are right, currently ggbio only supports summary of mismatch
coverage plot and barchart(?stat_mismatch), but looks like what you
detailed short reads alignments visualization with mismatch bases
right on the reads, . It's possible, but not easy to do it
have to have two GRanges objects, one for alignment one for SNP, and
them layer by layer, the tricky part is assigning each reads fixed
level, so snp can be plotted on the right position. I will NOT
you to do this, it's probably not worth taking time doing it. I need
implement this features in some easy way.
The tricky part is that there are different modes, 1. show reads as
rectangle, and color mismatch as segment 2. show SNP as nucleotide
A/C/T/G.., 3. show sequence detail for each alignment. those depends
zoomed level and even coverage, and I guess most time you don't want
bases for every reads...
Just curious for future ggbio development, are those modes want you
are you just using bam files here? no VCF files involved right?
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..
> Does someone of you have a good way to do this or found another
> that works for R/bioc?
> Best wishes
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