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Recent Replies
Comment: Harmony integration group.by.var parameter
by
Picasa
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640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq)
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ATpoint
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That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation
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peanut
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thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon
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Tonya S.
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Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon
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Rob
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If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
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I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
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> I don't know how widespread these issues are outside of JGI.
Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
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Supporting figures, taken from some slides I prepared for internal use.
HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
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This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★
17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ?
More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴
640
Thanks jared.andrews07 for your answer.
So, you are suggesting to use only "Donor" in the integration?
```r
RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
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I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
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Thank you for your comment and sorry if this question might be so basic.
How can I normalize the number of cells?
If I am not wrong the i…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
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Deepthi
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I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
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