Parameter suggestions for fixing misplaced scaffold

[Dikaryotic]

Hi,

I've used RagTag to scaffold my assembly against a decent reference and the results in general look good. However there is one pseudochromosome that appears to have been scaffolded incorrectly as it has a telomeric region placed about 500,000 bp into the scaffold, followed by a gap. Would you have any suggestions for parameters that could be tweaked to fix this?

I'm not 100% certain that it's actually a missassembly, but the results look dodgy so I thought I'd ask for help!

[damioresegun]

I've been having something similar too. On my end, it turned out to be due to chimeric contigs which RagTag doesn't seem to be able to do? So I fixed mine by doing RagTag first then putting the output of that as the input of RaGOO. Its not perfect for every use case but it fixed most of the weird misplaced scaffolds I had

[malonge]

Hi there,

It all really comes down to the alignments. I suggest you run with --debug and you can compare the alignments for particular contigs across the different paf files. The "merged.paf" debugging file shows the final alignments used for scaffolding. I suggest you find the contig containing this telomeric sequence and see where it aligns in the reference.

@damioresegun have you tried correcting the contigs first with ragtag correct? I would like to see if we can address your issue as well since RaGOO will eventually be archived. If you are interested, please feel free to open up another issue.

Thanks, Mike

[damioresegun]

@malonge I've detailed it in Issue #30