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Recent Replies
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
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I think when you give indent to seuObj :
Idents(seuObj) <- 'RNA_snn_res.0.1'
You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
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In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
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In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
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> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended
If they sent data that is not what you…
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I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K).
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Answer: Sequence read length shorter than flow cell specification
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It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
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you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator :
VariantAnnotator …
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by
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Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
by
jkim
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cross posted in bioconductor.
[https://support.bioconductor.org/p/9157968/][1]
[1]: https://support.bioconductor.org/p/9157968/
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Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
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Hi Dan,
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QX
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I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
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I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
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the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
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> I would like to ask why they may require the bam file for this function?
hum.. if you want to add the coverage, where do you think gatk …
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