I have run LACHESIS to scaffold human genome contigs using a Arima v1 Hi-C reads. I know positively that those reads create chromosome level scaffolds. Indeed LASECHIS produces significant clusters of contigs but do not get to order any of them. I have played around with the different parameters used in the publication supplementary online materials without making any difference.
Is there any obvious reason you could possibly think responsible for not getting any single ordered set of contigs.
Hello,
I have run LACHESIS to scaffold human genome contigs using a Arima v1 Hi-C reads. I know positively that those reads create chromosome level scaffolds. Indeed LASECHIS produces significant clusters of contigs but do not get to order any of them. I have played around with the different parameters used in the publication supplementary online materials without making any difference.
Is there any obvious reason you could possibly think responsible for not getting any single ordered set of contigs.
Many thanks Jorge