zhangrengang
zhangrengang
@mrmrwinter According to the heatmap and PCA plot, Subphaser is failed to your assembly. From the Hi-C map, there are many assembly errors. Some contigs are mis-joined into one chromosome...
 @mrmrwinter Three cases as shown in arrows: the green indicates clear boundary between chromosoms that should be split; the yellow indicates contacts that should be joined; and the blue...
@mrmrwinter You can have a look on this paper: > Dudchenko O, Batra S S, Omer A D et. al. De novo assembly of the Aedes aegypti genome using Hi-C...
@mrmrwinter OK. Looking forward to your feedback.
这是没分开，如果组装没问题，就很难再改善了，有可能是同源三倍体，用这个方法分不开。如果可用kmer很少，可以试试减少配置文件里的同源关系（原先17行3列改成比如10行3列+21行1列的），并降低-q参数（比如降到100）。
@YuChrming, Your genome has too few differential kmers between subgenomes. It may be artifactual or natural. My suggestions (refer to the [Supplementary Material](https://nph.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fnph.18173&file=nph18173-sup-0001-SupInfo.pdf)): 1. Check the HiC contact map whether...
1. Have you removed the check point files (tmp/*ok) before re-run or used the `-overwrite` option? 2. What are the evidences for `allo`?
Can you show me the whole log and the plots produced by subphaser? I suspect that the genome is not well phased.
As clearly shown by the results, the subgenomes are not well assigned, because there are too few differential kmers between subgenomes. It may be artifactual or natural. My suggestions (refer...
Maybe the PYTHONPATH is not set properly. Do you have added "${NEW_PATH}/lib/python3.9/site-packages/" to PYTHONPATH?