If I run rectangle directly on my epiread it says: "[main_rectangle:79] Error, rectangle cannot cross chromosomes". The manual does not say the input has to be chromosome split.
If I run it on a subset of the epiread in chr1, it finishes but the output looks weird. The output simply appends a 9th column to the epiread file and the 9th column is a string of 1,020,893 Ns.
If I run rectangle directly on my epiread it says: "[main_rectangle:79] Error, rectangle cannot cross chromosomes". The manual does not say the input has to be chromosome split. If I run it on a subset of the epiread in chr1, it finishes but the output looks weird. The output simply appends a 9th column to the epiread file and the 9th column is a string of 1,020,893 Ns.
My epiread input:
My rectangle command-line: