convert.sh does not produce a .hic file in the appropriate format for juicebox #154

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1. yuzhenpeng commented on Dec 2, 2021

   

   yuzhenpeng

   on Dec 2, 2021

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   I met the same problem. How to deal with it.
2. oneillkza commented on Dec 2, 2021

   

   oneillkza

   on Dec 2, 2021

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   I mean, the answer from the Juicebox team seems to be "Don't use SALSA if you want to edit your assembly in Juicebox".

   Or alternately to run the final assembly from SALSA through the entire Juicer workflow to try to get to something compatible with Juicebox. But the Juicer workflow is a nightmare to get running.

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3. yuzhenpeng commented on Dec 3, 2021

   

   yuzhenpeng

   on Dec 3, 2021

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   I mean, the answer from the Juicebox team seems to be "Don't use SALSA if you want to edit your assembly in Juicebox".

   Or alternately to run the final assembly from SALSA through the entire Juicer workflow to try to get to something compatible with Juicebox. But the Juicer workflow is a nightmare to get running.

   juicebox V 2.X can open the .hic generated by SALSA.
4. oneillkza commented on Dec 3, 2021

   

   oneillkza

   on Dec 3, 2021

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   Juicebox itself can open the .hic file and visualize it, but the parts of Juicebox for editing the assembly (aka "Juicebox assembly tools" or JBAT) require an "assembly" .hic file, which the file produced by SALSA is not.

   Here are some quotes from the Juicebox developer, from the issues I linked in the OP:

   Thanks for a detailed description of the issue you are experiencing. Closing since this is not a bug. Looks like you are trying to use JBAT on a sandboxes, non-assembly hic file. Please consult Genome Assembly Cookbook (dnazoo.org/methods) on 3D-DNA tool suite usage. Thanks, -Olga

   We do not offer any support for Salsa since we are not developers of that tool: my guess would be that the hic file is not in the right ‘assembly’ format.

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5. yuzhenpeng commented on Dec 3, 2021

   

   yuzhenpeng

   on Dec 3, 2021

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   Okay, Thank you very much.

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6. c2997108 commented on Mar 9, 2022

   

   c2997108

   on Mar 9, 2022

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   I have created a tool to edit a contact map by directly reading SALSA output files (scaffolds_FINAL.agp, alignment_iteration_1.bed and assembly.cleaned.fasta). It only displays at the window size of the first specified resolution (default is 100 Kbp), but it seems to work faster. At least it worked well enough for me.
   https://github.com/c2997108/SELDLA-G/blob/master/README.md

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7. jacquelinemattos commented on May 10, 2022

   

   jacquelinemattos

   on May 10, 2022

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   Has anyone solved this problem?