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Hello,
I've been using protein k-mers from sourmash to compare single-cell RNA-seq profiles across different species. I'm curious to benchmark `dashing` for this purpose as well.
Warmest,
Olga
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I have a weird issue with ploidyplot. It was working fine before:
```
PloidyPlot -e12 -k -v -T38 -o/smudgeplot/kmerpairs /smudgeplot/FastK_Table
Activating conda environment: .snakemake…
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Per: https://github.com/ctb/2022-sourmash-sens-spec/blob/main/fracminhash-runs-simulate.ipynb
```
in M=100 k-mers, p of finding at least one hash is: 63.43% - scaled=100
in M=200 k-mers, p of fin…
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per https://github.com/sourmash-bio/sourmash/issues/1833#issuecomment-1033860432, it seems like we should investigate this and figure out if it works, and if so, how well.
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Hi,
I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
```
# extract consensus sequences from profiles
…
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Hi,
After finding some relevant consecutive 31-mers, we would like to repeat the workflow with k=41 in order to focus our search. The template config.yaml discourages this, and it becomes clear fr…
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![image](https://user-images.githubusercontent.com/7740734/138983624-7330ec4e-43e7-4638-8804-bd22b48d94b3.png)
Your results show that the correlation btwn # protein k-mers and # genes per genome is…
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Could the number of k-mers in the query be included in the output so the user can calculate the percentage of the query in each dataset (or provide the percentage as well)?
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Hi again Dr. Rhie,
I'm having a great time using merqury to asses quality and completeness of different versions of our assembly. It's an awesome tool and it is allowing us to make more informed dec…
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I'd like to understand why kmc gives an empty output for several genomes.
The genome I downloaded and tried to analyze was [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/067/135/GCF_001067135.1_…