Forcing merge of scaffolds

[chopra29]

Hi,

I have improved assembly using several maps and would like to see HiC plot based on the final assembly. I used -m no option to avoid breaking down the assembly but it forces the merging of 3 large scaffolds. Is there an option to avoid this merge.

Ratan

[skoren]

I assume you're trying to run convert.sh and don't want to scaffold at all? You should be able to specify no mappings (an empty bed file) for scaffolding but this really isn't what Salsa was designed for. There are other HiC visualization tools (like higlass, Juicebox, etc) that you could use to visualize HiC interactions on a finished assembly.