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

[LIZW2019]

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]

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 [email protected] 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

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