Hi everyone, I'm trying to assemble transcriptome using RNAseq reads via scripture package. I've prepared sorted sam file, chr fasta and size files and ran the program according to authors instruction here . I'm getting a weired error though that says scripture needs a windows size. reading the manual I understood that providing "windows size to scan" is optional and scripture could determine windows scan size by itself but I'm getting this error as if its mandatory. apparently I have to provide it myself I have no idea how to specify a size that is accurate! there is no clue in scripture website and paper just
"-windows: Comma separated list of fixed size windows to scan. By default Scripture identifies regions of uninterrupted coverage and uses this regions to segment the data. However, in some cases it is usefule to specify alternative or multiple window sizes
" I need some clarification on how i should specify windows size and why scripture is asking me to provide such a thing. thanks
