search

VGP / vgp-assembly

VGP repository for the genome assembly working group
Other
185 stars 51 forks source link

asset bionano problem #51

Closed zhoudreames closed 3 years ago

zhoudreames commented 3 years ago

in my project,and human CHM13 v1.0 assembly,I used asset to evaluate the structure of assembly,but it both present a problem about binano low support region ,the no good result show in blow: in CHM13 v1.0 Assembly: image in the red square,the binano low support region covered the whole chromosome.I used your recommend parameter that requires regions to have at least 10 molecule coverage or 0.5 x (average molecule coverage). i dont know why ,and i try to change the parameter into 0.3,0.2,0.1, it didnt work. can you help me? and this phenomenon also present my project ,i think this is common problem . this problem show in blow: image

zhoudreames commented 3 years ago

@mcshane @skoren @Arkarachai @godotgildor I am very sorry to disturb you ,i am very interesting your method,thank you for your help !

arangrhie commented 3 years ago

Hi @zhoudreames , we noticed the bionano coverage dropouts too. It seems like it is due to the lack of sequence motif bionano is using for labeling. Note the centromeric sequence has a very limited sequence pattern compared to the rest of the genome.