Visualization and editing SLASA scaffolding fasta file

pubudu nawarathna

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Feb 8, 2021, 1:20:17 AM2/8/21

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Hello,

I used SALSA to create the fasta file from hic reads and draft genome assembly. Then I used juicer tools pre to create a hic file and juice box to visualize the hic file. However, I got many scaffolds and misassemblies. I need to edit them using Juice Box. But I do not have an assembly file. Is there a way to create an assembly file using Juicer? I do not have a merged_nodups.txt file.

Thank You,

Best,

Pubudu

Olga Dudchenko

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Feb 8, 2021, 2:33:23 AM2/8/21

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Hello Pubudu,

We do not offer support for SALSA as we are not the developers of that tool. For instructions on how to use our tools for assembly, please see the Genome Assembly Cookbook, hosted at dnazoo.org/methods.

Best,

Olga

pubudu nawarathna

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Feb 8, 2021, 3:57:56 PM2/8/21

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Dear Olga,

Thank you for the response. Since we used Arima Genomics library preparation kit not the in-situ HiC we may not be able to run the Juicer since it does not generate merged_nodups.txt file. Is that correct or is there a way to run it?

Thank You,

Best,

Pubudu

Olga Dudchenko

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Feb 9, 2021, 11:27:37 AM2/9/21

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Hi Pubudu,

Arima kit is an in situ Hi-C kit. You can process the data just like you would any other Hi-C experiment. See many threads on this forum using Arima data.