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Hi there,
I was running `velocyto run10x -m /ceph/project/....../mm10_rmsk_chrMTGTF.gtf /ceph/project/........../10x_scRNA_704-187_CD8P_GEX /ceph/project/borrowlab/shared/scRNASeq_blood_220210/xen…
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If we can't do a great job with cell types, what can we do with assigning tumor/normal status?
Especially inferring CNV status.
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I have created the copy number input file, normal file as well as the tumor file. I followed the format according to the Manual instruction.
When I only run RunTHetA with just the copy number file, i…
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Hello,
I am trying to annotate a reptilian genome that has a fairly good scaffolded assembly (N50 = ~215MB; 1,966 scaffolds). Genome busco completeness is ~93%
I have RNA-seq data from a pooled se…
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See also #28 (comparing clusters to Allen cell types)
- Nature Biotech paper (2018): [Dimensionality reduction for visualizing single-cell data using UMAP)](https://www.semanticscholar.org/paper/Di…
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Hi there,
I have a couple of questions...
1) I am running SwiftOrtho on around 700 bacterial genomes. I substituted step 1 with a diamond run (with a suitably increased max-hits pram) and by run…
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When sketching sequences with `N` in them and using the `--check-sequence` option I get the following exception:
```
sourmash.exceptions.Panic: sourmash panicked: \
thread 'unnamed' panicked with…
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Dear developers,
When I run `dRep` with the `-nc` parameter set to `0.6`, the program generates most output correctly but the PDF files of the secondary clustering dendrograms and MDS cannot be ope…
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Using a random subset of 21,562 protein signatures from prodigal translation of pigeon1.0 --
1. threshold = 0.1; protein k=7; batch size = 5000;
`time python find-founders.py -k 7 --moltype prot…
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**Submitting author:** @Juke34 (Jacques Dainat)
**Repository:** https://github.com/Juke34/AliNe
**Branch with paper.md** (empty if default branch): main
**Version:** v1.0.0
**Editor:** @jromanowska
**…