Final files for interpretation

[samyuktha Senthil]

Hi,

  Thanks for this wonderful tool, it is my first time using 3d-DNA. I have a small doubt, which is the scaffolded assembly and the corresponding .hic file for visualisation? There are xx.final.hic, xx.final.assembly files and I read on the manual that these files can be used for visualization and JBAT curation. However, there are also xx.FINAL.fasta and xx.FINAL.assembly files, so technically, the xx.FINAL.fasta is the scaffolded assembly fasta file but I do not see a xx.FINAL.hic file!

 This is quite confusing, should I generate a xx.FINAL.hic using Juicer pipeline with xx.FINAL.fasta as the input and xx.FINAL.assembly can be used to visiualize chromosome structure or is xx.final.hic sufficient? Any help is greatly appreciated!

Thanks and regards,

Sam