Comments (2)
Dear @huangyizR,
Honestly, I don't know. But I guess you could do the following:
- IGV: If your purpose is only to get a visual representation, in IGV discordants are represented in green, and soft-clipped and hard-clipped reads are represented as shorter, partial hits.
Another option would to use Gviz (https://bioconductor.org/packages/release/bioc/html/Gviz.html) to plot discordant and split reads. I personally like Gviz a lot and have used it for a bunch of papers.
I hope this helps
Best,
Inigo
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I am closing this one. Feel free to reopen
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