search

shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
Other
76 stars 33 forks source link

get a very big clusters #22

Closed liufuyan2016 closed 7 years ago

liufuyan2016 commented 7 years ago

I have recently used LACHESIS for the long read assemblies(the assembly contig N50 10Mb). I get a very big clusters(60Mb,50% genome) no matter what the parameter adjusted. Could you help me?

tangerzhang commented 7 years ago

Hi liufuyan2016, Have you solve your problem? I am having the same problem when using LACHESIS for HiC scaffolding. I got actually two very very big clusters (500M). I re-open this issue as I have no idea how to solve this. Could any one help me with this issue? Thanks!

kfletcher88 commented 5 years ago

Hi, I know this is nearly two years old, but do you guys have a solution for this? I was thinking to down-sample the data to see if that increases the number of large clusters. At the moment I am obtaining 99.58% of the assembly in a single cluster. Thanks

tangerzhang commented 5 years ago

The solution is to use 3D-DNA pipeline to correct the mis-joint contigs.