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Recent Replies
Answer: ScRNA data question
by
Bioinfotec
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10
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…
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> 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…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
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840
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).
| …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
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…
Comment: Why gatk VariantAnnotator required bam and coverage files
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you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator :
VariantAnnotator …
Comment: GAPIT p-value significance threshold
by
ginellegrenier
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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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170
cross posted in bioconductor.
[https://support.bioconductor.org/p/9157968/][1]
[1]: https://support.bioconductor.org/p/9157968/
Comment: ScRNA data question
by
bk11
★
2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
by
sp
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Hi Dan,
I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
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…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
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GenoMax
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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…
Comment: Figures are disappeared from html report of SnpEff
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Pierre Lindenbaum
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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
by
Pierre Lindenbaum
161k
> 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 …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴
30
By following above approach I got this
![enter image description here][1]
[1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
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0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
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