I would like to kindly ask for some help from the awesome Biostars community in regard with using CNEFinder (https://github.com/lorrainea/CNEFinder). This tool can perform CNE searches on whole chromosomes/scaffolds. Because I would want to use an assembly with 675 scaffolds and would want to iterate over all of them it would be easier if I were to combine said scaffolds into one giant scaffold. While doing this I would need to maintain the exonic coordinates as those are not masked when performing the search. The exonic coordinates should be given to CNEFinder in the following format:
seqnames start end width strand CAJNDQ010000011.1 30197297 30197305 9 + CAJNDQ010000011.1 30198128 30198367 240 +
If you have any suggestions around this could you please share it? Thank you in advance.