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@NaotoKubota
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Hi Skipper maintainers,

Thank you for creating this wonderful tool!

I am trying to analyze my eCLIP data from mouse samples by Skipper and got an error in the make_unscaled_bigwig and make_scaled_bigwig rules with this message:

output/bedgraphs/unscaled/plus/N1_IP_2.unscaled.plus.bg is not case-sensitive sorted at line 2405117.  Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C,  or bedSort and try again.

Thus I suggest using sortBed instead of the UNIX sort command. It is working on my end.

Best,

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