need to map scaffolds to chromosomes: have mashmap outfile

Question

[truebeliever24]

Hi,

I have many genomes that are aligned to a reference genome composed entirely of scaffolds. I used mashmap to produce the mappings of these scaffolds to a fully sequenced, close relative that has chromosomes assigned (mashmap.out file). Now I need to use the mapping output from mashmap to actually find the locations of scaffolds on the chromosomes, so that I know which chromosome contains each scaffold. The goal is to be able to sliding window analyses for several summary statistics and to be able to analyze patterns across chromosomes. Can somebody please help me with this? Thank you!