Francesco Cicconardi

Wait a minute @tanghaibao, those inverted contigs are single contigs. This is the synteny after the LM scaffolding. I cannot show you the LM dot-plot because AllMaps fails to plot...

I've been talking with Pasi Rastas, the guy who developed Lap-MAP3. He said to me "Allmap's default behavior is not very good; for some reason it does not orient all...

"First, we notice that LA reports five chimeric scaffolds for theyellow catfish data (scaffolds 44, 75, 123, 165 and 230), whereasALLMAPS on default puts all contigs into at most one...

LA is as easy to use as maneuvering a helicopter. F

Hi @malonge, I see your point. I think I also have to be sure that those fragments (contigs) are not still overlapping, which I think it's the case. So far...

Dear @spond, Thanks a lot, that makes sense, and yes, I was already thinking to run RELAX to understand the direction! Thanks a lot! F

Hi @KatharinaHoff Here are the files: [braker.log](https://github.com/Gaius-Augustus/BRAKER/files/6027928/braker.log) [crftraining.stderr.txt](https://github.com/Gaius-Augustus/BRAKER/files/6027929/crftraining.stderr.txt) [crftraining.stdout.txt](https://github.com/Gaius-Augustus/BRAKER/files/6027930/crftraining.stdout.txt) Thanks F

Hi Katharina, Any update? Cheers F

I made a script of my own. F

I see, Is there a step I can use, or I have to re run the analysis with the flag onff? Thanks F