search

aidenlab / 3d-dna

3D de novo assembly (3D DNA) pipeline
MIT License
203 stars 56 forks source link

run-asm-pipeline-post-review.sh generate .hic file does not look the same as I have adjusted. #66

Open LIZW2019 opened 4 years ago

LIZW2019 commented 4 years ago

Hi, I used Juicerbox to adjust my assembly and get to the final figure I think is prefect. But after I run the run-asm-pipeline-post-review.sh and get the final.hic and its corresponding assembly file, and i put them in the Juicerbox to check. I find the hic plot looks different from the one I adjusted before, even with large translocation mistakes. What should I do?

Best wishes, LIZW

dudcha commented 4 years ago

Hi LIZW,

I’m sorry to hear that. Most likely this means you’ve used the wrong file when saving/restarting the review process. If this is the case nothing I’m afraid can be done. When saving and restarting the review it is important to keep the original assembly file intact and use then when first loading the assembly. The details are outlined in cookbook.

Thanks, Olga

On Oct 22, 2019, at 9:33 PM, LIZW2019 notifications@github.com wrote:

 Hi, I used Juicerbox to adjust my assembly and get to the final figure I think is prefect. But after I run the run-asm-pipeline-post-review.sh and get the final.hic and its corresponding assembly file, and i put them in the Juicerbox to check. I find the hic plot looks different from the one I adjusted before, even with large translocation mistakes. What should I do?

Best wishes, LIZW

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.