User: Payal

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Payal70
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@payalpb_me
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Posts by Payal

<prev • 35 results • page 1 of 4 • next >
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Is Pseudotime analysis most applicable to time-series experiments?
... Hi, This is a theoretical question. Is pseudotime analysis generally applied to time-series type experiment? Or can also be applied for a single time point. Thanks, Payal ...
single-cell rna-seq written 6 hours ago by Payal70
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Choose root nodes in Monocle3
... Hi, How to to choose root nodes programmatically for Monocle3 in the order_cells step? The tutorial is good but very experiment specific. Mine is not a time series experiment. Its an exploratory analysis. Also whats the difference between root_pr_nodes and root_cells for the function order_cells? ...
trajectory single cell rna-seq written 6 weeks ago by Payal70
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Comment: C: Unequal sample sizes Deseq2
... Thanks a lot. I did plotPCA with vst and there were clear batch effects for n of 3. After removing the bad sample and performing DEG with n of 2, I again did plotPCA and then I saw clear PCA plots. ...
written 8 weeks ago by Payal70
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Unequal sample sizes Deseq2
... Hi, I have two groups with 3 replicates each for differential gene expression analysis. **Control** - Sample1 - Sample2 -Sample3 **Experiment** -Sample1 -Sample2 -Sample3 However, Sample3 in Control has high duplication rate almost double reads than other samples. For differential gene expres ...
rna-seq sequencing written 8 weeks ago by Payal70 • updated 8 weeks ago by ATpoint35k
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Downstream RNA seq analysis
... Hi, What are the most common donwstream analysis steps and tools for RNA seq analysis, after getting the diferentially expressed genes? I know this is a very generic question and its supposed to be fine tuned to particular research, but in general what are your goto tools and pipelines for a stand ...
rna-seq written 3 months ago by Payal70 • updated 3 months ago by dsull1.3k
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Answer: A: htseq-count cannot find pysam
... `conda install pysam` worked for me. ...
written 4 months ago by Payal70
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Comment: C: Cellranger data to Monocle Pseudotime
... Yes I used normal cellranger aggr to aggregate samples but they used to have this cellranger R kit to easily transform data into an R matrix type object, which they no longer support. So I am having this confusion because now they output everything as barcodes.tsv.gz, features.tsv.gz and matrix.mtx. ...
written 4 months ago by Payal70
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Cellranger data to Monocle Pseudotime
... Hi, How to convert 10X data to do psedotime analysis using Monocle. All the tutorials in Monocle point to cellranger kit which has been deprecated. I followed - https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices and https://kb.10xgenomics.com/hc/en ...
single cell rna-seq sequencing written 4 months ago by Payal70 • updated 4 months ago by jared.andrews075.5k
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Comment: C: FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
... Thank you! This is helpful. I have a combined dataset (control vs treatment ). I was following this - https://satijalab.org/seurat/v3.1/immune_alignment.html tutorial. I got confused after the FindConservedMarkers step. In general on what basis should we select the marker genes to draw the featur ...
written 6 months ago by Payal70
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FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
... Can someone please explain the difference between FindConservedMarkers and FindMarkers. As per definition: > FindConservedMarkers- Finds markers that are conserved between the groups 1. But does that mean that the genes are similarly expressed between groups/conditions or genes are differenti ...
single-cell R next-gen rna-seq written 6 months ago by Payal70 • updated 6 months ago by jared.andrews075.5k

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
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Popular Question 2.8 years ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How to download raw sequence data from GEO/SRA

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