User: bernt.popp

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bernt.popp0
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Posts by bernt.popp

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Comment: A: Gviz off-by-one with STAR BAM
... Hey, the BAM subset for that region with samtools: https://www.dropbox.com/s/k4qjcx9o6ntdovj/subsetforGviz.bam?dl=0 The index: https://www.dropbox.com/s/0wtsclep3fjp670/subsetforGviz.bam.bai?dl=0 The error is reproducable on my system with this BAM. Best, Bernt ...
written 8 months ago by bernt.popp0
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Gviz off-by-one with STAR BAM
... Dear Gviz guys,   Unfortunately I am getting a weird off-by-one error when trying to plot coverage and reads from a STAR alignet BAM file. This error is only present in Gvit and not in IGV: https://www.dropbox.com/s/phh49m83iye0kmz/Gvizoffbyone.jpeg?dl=0 https://www.dropbox.com/s/3gpu5l3pviznznx ...
coverage gviz bam star off-by-one written 8 months ago by bernt.popp0 • updated 8 months ago by Martin Morgan ♦♦ 20k
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Gviz sashimi read count
... Hey, I would like to plot the count of spliced reads supporting the junction above the splice bezier-curve, similar to the original sashimi plot now integrated in IGV. Is there an option in Gviz for this?   Best, Bernt ...
gviz bam read counting sashimi plots sashimi written 8 months ago by bernt.popp0 • updated 8 months ago by Robert Ivanek350
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GVIZ junction plot without bam
... 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 sequ ...
gviz junction intropolis sashimi written 15 months ago by bernt.popp0 • updated 14 months ago by florian.hahne@novartis.com1.5k

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