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Dear team,
I would like to clarify if the --renz parameter in tadbit map supports the restriction site for the
ARIMA kit (https://arimagenomics.com/products/genome-wide-hic/) - ^GATC,G^ANTC.
If …
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Hi,
I have some questions about pruning step (how heterozygous alleles be partitioned...) and input/output files.
1. What is the difference between collapsed regions and chimeric contigs in prunin…
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Hi @kirilenkobm @MichaelHiller,
I `wget` [https://github.com/hillerlab/make_lastz_chains/archive/refs/heads/main.zip](https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2F…
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Following a conversation with @rob-knight @gregcaporaso @antgonza and @cuttlefishh, we came up with a preliminary list of algorithms that would be fantastic to include. Education and optimized version…
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Hi,
This follows the issue #80
The problem was the group assignment to the chromosomes homologous groups. We are working on the assembly of a tetraploid potato. If we do not separate the contigs i…
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Looking at realSFS dadi, I notice that it uses the outer product of the 1d SFS as a prior for calling bins/site, rather than accepting a "joint" prior that is >=2 dimensional. I suspect this isn't a g…
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### Operating System
CentOS 7
### Other Linux
_No response_
### Workflow Version
v2.10.1-g4c2c583
### Workflow Execution
Command line (Cluster)
### Other workflow execution
…
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HelIo, I used hifiasm -o rz.asm -t 30 --n-hap 4 --ul ONT.fastq.gz hifi.fastq.gz to assemble a tetraploid genome, didn't Distinguish haplotypes, would you tell me there will be 2 or 4 p_ctg.gfa in the …
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- [x] discuss shortly the pipeline and its configuration with MS
- [x] check fastp documentation bc paired end (PE) needs additional sequence_r parameter here https://github.com/epigen/atacseq_…