I had actually tried to run sequenza.extract on seqz.data but receive an error:
> test <- sequenza.extract(seqz.data) Error in pipe(paste("gzip -d -c", file, "| cut -f 1,6,10")) : invalid 'description' argument
Can anyone explain this to me in a bit further detail? Is there just something wrong with my data files or am I just making a poor assumption on what sequenza is actually doing? If sequenza.extract(data.file) is correct for real data then what purpose does the GC normalization steps serve?