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Does not work with chromosome names 1, 2, 3, ... #5

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MarekGierlinski opened this issue Apr 12, 2023 · 1 comment
Closed

Does not work with chromosome names 1, 2, 3, ... #5

MarekGierlinski opened this issue Apr 12, 2023 · 1 comment

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@MarekGierlinski
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MarekGierlinski commented Apr 12, 2023 •
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When chromosomes are named 1, 2, 3... (not chr1, chr2, chr3, ...) the run_decoden script crashes with error:

pyarrow.lib.ArrowInvalid: ("Could not convert '9' with type str: tried to convert to int64", 'Conversion failed for column seqnames with type object')

I confirmed this by changing my chromosome names into chr1, chr2, chr3, ..., upon which the script completed with no errors.
@ntanmayee
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This issue is fixed with using deeptools for preprocessing, fixed with commit 256551c

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@ntanmayee @MarekGierlinski