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Hi-
I submitted a bug report a couple of weeks ago to the LeafCutter github, but putting it here in case this is the better place.
davidaknowles/leafcutter#217
I was having the same issue as davidaknowles/leafcutter#98, in which my genes were all labelled as 1 or 2. I have discovered the source of the issue, which is that the annotation files downloaded using the leafcutter/leafviz/download_human_annotation_codes.sh script is incorrect for hg38. The genes are labelled as either "1" "2" or "3" instead of their real gene name, causing downstream errors for LeafViz.
Could a corrected version please be uploaded to dropbox?
Thanks!
-Rachel
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