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.
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_bigwigandmake_scaled_bigwigrules with this message:Thus I suggest using
sortBedinstead of the UNIX sort command. It is working on my end.Best,