Jay Ghurye comments

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                                            Jay Ghurye

Adding a new genome

Hi, Was this issue resolved? I am getting the same error. I ingested a new genome with `--coordSystem genomeName`. I can see the coordinate system, but when I try to...

Link data not exhausted. fixable inversion and unlinked scaffolds

SALSA shouldn't give different results with different input runs with the same parameters. Was it run to completion in all the runs?

empty alignments_sorted.txt file while generating .hic file

Did you run it with -m yes option? If not, then you can use the bed file that you provided to SALSA as an input to the .hic file creation...

Post processing steps after SALSA

1. Improving scaffolding is an open research question. 2. What kind of statistics you are looking to generate? 3. Currently we don't support misassembly correction for SALSA2 output through juicebox.

Bad result because low quality Hi-C library?

What's the input N50 of the assembly? Also, you would want to look at ALL_INTER as those are the inter-contig links that will be used for scaffolding. I do agree...