EarlyEvol

Olga, No problem on the delay, I am also traveling right now. I ran 3d-dna in default mode, so should be haploid mode. Here is the code I used. ```...

Yes, two assemblies are having trouble related to the .hic encoded genome length. I'm happy to share the files with you. What is you preferred method? Thanks so much, Earl

Olga, Now I have to apologize for the delay. I just got back from some conference travels. I have sent a link to your email with the merged_nodups and the...

Haha, well dang. That is a major problem. I added a log file (in the linked folder) from 3d-dna and I don't see anything that makes it look like scaffolding...

Edwin, Thanks for the speedy reply! I have merged in both directions. Each time busco genes are lost similar to above. basically the merged.fasta is always in the middle of...

Well, I have figured out part of my confusion. In the [QM pub](https://academic.oup.com/nar/article/44/19/e147/2468393), it states "In the final step, the ordered chain of contigs found in the previous step is...

hmm...could you speak a little more about how this process works? If there are inconsistencies between assemblies, i.e. contig QueryA and contig RefA align for the first half of their...

Edwin and Mahul, Also, the large amount of duplicated BUSCOs after running QM is a little disconcerting, and like #15, every run of QM seems to increase the duplication rate....

Alright, I put a post on Biostars asking if anyone has written one. Seems like it should have been done before, especially with people getting all sorts of different data...

fyi Got the standalone HiCMatrix install to play nice with HICAssembler to be able to use HiCExplorer 3. All from a fresh miniconda3 install with pip ``` git clone https://github.com/deeptools/HiCMatrix.git...