Question: GVIZ junction plot without bam
0
gravatar for bernt.popp
2.8 years ago by
bernt.popp0
bernt.popp0 wrote:

Hi,

is there a possibility in GVIZ to plot a junction track without a BAM file using only junctions and a desired coverage?

I would like to plot the junctions from the intropolis (https://github.com/nellore/intropolis/blob/master/README.md) resource as a comparision for a Patient/Control cDNA sequencing experiment. My initial solution was to generate pseudo bams containg artifical reads covering the respective junctions as many times as the sum of all samples in intropolis.

Is there a simpler way?

Thanks for any ideas!

Bernt

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UPDATE:

Basically a functionallity to replace the lines in an AnnotationTrack with arches or chevrons (like in ggbio "geom chevron" or "geom arch") would do the trick. Especially if one could also change the linke thickness. Can't find any similar function in gvuz though.

ADD COMMENTlink modified 2.8 years ago by florian.hahne@novartis.com1.6k • written 2.8 years ago by bernt.popp0
Answer: GVIZ junction plot without bam
0
gravatar for florian.hahne@novartis.com
2.8 years ago by
Switzerland

Hi Bernt,

this is currently not supported in Gviz. Plotting junctions is a feature of the AnnotationTrack class, and thus we need the BAM file to extract the alignment information from. I agree that a bit more flexibility in the customisation of the lines that connect features would be useful. I'll try to take a look at this for one of the next release. Sounds like we should be able to port the code from the AnnotationTrack class.

Florian

ADD COMMENTlink written 2.8 years ago by florian.hahne@novartis.com1.6k
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