User: thackl

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thackl0
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Posts by thackl

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Comment: C: Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
... Yes, that's what I was afraid of. But rather than including the entire stretch of unmapped bases (as IGV does and which needs to be accounted for in stacking etc), would it be possible to just color or mark the start/end of  a read if the cigar starts/ends with an S/H? ...
written 3.4 years ago by thackl0
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Comment: C: Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
... I like the idea of splitting into clipped/non-clipped reads. But as you said, it is a practical, but not really satisfying solution :) ...
written 3.4 years ago by thackl0
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Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
... I am using Gviz to visualize mappings of PacBio data (bam files) onto contigs. I was wondering if there is any way to display soft-clipped bases at read ends, or at least indicate reads with soft-/hard-clipped ends. That would help a lot in spotting structural variations and potential misassemblies. ...
gviz bam pacbio written 3.4 years ago by thackl0 • updated 3.4 years ago by florian.hahne@novartis.com1.6k

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