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stianlagstad / chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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Reading fusion seq #23

Closed plijnzaad closed 5 years ago

plijnzaad commented 6 years ago

STAR-fusion >= 1.2.0, when run with --denovo_reconstruct has a column FUSION_CDS in output file star-fusion.fusion_predictions.abridged.annotated.coding_effect.tsv which contains the fusion sequence. This PR extracts it and adds it to the fusion object (in addition to setting attribute inframe ad also adding FFPM and annots to fusionToolSpecificData )

plijnzaad commented 6 years ago

Note that this PR is deliberately against a much older commit (close to stainlagstad's master), as it is independent of my recent FusionInspector PR's

stianlagstad commented 5 years ago

Closing in favor of https://github.com/stianlagstad/chimeraviz/pull/56. Thank you @plijnzaad !