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 2.1 years 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 2.1 years ago by bernt.popp0 • updated 2.1 years ago by Martin Morgan ♦♦ 23k
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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 2.1 years ago by bernt.popp0 • updated 2.1 years ago by Robert Ivanek590
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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 2.6 years ago by bernt.popp0 • updated 2.6 years ago by florian.hahne@novartis.com1.6k

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