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Hi,
When I ran scAbsolute with the default ploidy window I noticed that a lot of cells (~50%) had copy number of 1 across the genome, which is not something we expect to see in the samples (blood c…
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I assume that if this is haploid data, we don't need a call_genotype_phased array to show that the data is phased? Unless the suggestion is that haploid data without a call_genotype_phased array could…
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Hello,
I noticed that you've modeled eQTLs on the X chromosome and I'm wondering whether is possible to make predictions of overall expression for haploid individuals (i.e. men) using the "slope" c…
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In comparing output from the API and the CLI during the probgen workshop I noticed a discrepancy in the ploidy output through a conversion to vcf. I think the issue is on the CLI side.
Here's an e…
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### Description of feature
**Description**:
I am writing to request the addition of parameters for specifying haploid contigs and regions when detecting SNPs and Indels using DeepVariant in the nf…
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### Description of feature
It is unclear if this pipeline will work on any organism assembly?
Is it haploid genomes only?
Is it especially for bacteria?
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Hello,
I am interested in using the locator algorithm for haploid organisms. The help text says to file an issue.
Thank you,
Mike
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```
I am really excited about this resource. I am wondering if it can be used for
haploid organisms, and if this would require changing any of the pipeline?
```
Original issue reported on code.goo…
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Hello,
I would like to use bigsnpr to compare the output of clumping vs pruning in my snps dataset from Zymoseptoria tritici. As it is an haploid organism, and I have selected only bialellic snps, …
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Hi all,
we are assembling some haploid fungal genomes (using PacBio HiFi data). Would purge_dups be appropriate for removing contig overlaps in such an assembly?
Best,
Ricardo Ramiro