User: Bogdan

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Bogdan1000
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Palo Alto, CA, USA
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Posts by Bogdan

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Comment: C: scRNA-seq data at different time points
... Thank you. Yes, i have been using Conos, Harmony, Seurat3 pipelines for batch correction (as outlined in Seurat wrappers) : https://github.com/satijalab/seurat-wrappers I have came across Tempora for gene expression time series analysis, although I have not tested yet how it works on our data : h ...
written 4 weeks ago by Bogdan1000
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scRNA-seq data at different time points
... Dear all, please may I ask about your suggestions regarding the package(s) to use for the analysis of scRNA_seq data that has been collected at different time points (1,2,3,4,5) and to infer the disease / developmental trajectories on each cell cluster ? thanks a lot, -- bogdan ...
scrna-seq written 5 weeks ago by Bogdan1000 • updated 2 days ago by Biostar ♦♦ 20
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Comment: C: computing resources for scRNA-seq analysis
... just a note to add, the pipeline suggested by the authors : https://satijalab.org/seurat/v3.1/integration.html using a reference-based approach seems to be working well. To quote : "we present an additional modification to the Seurat integration workflow, which we refer to as ‘Reference-based’ ...
written 6 weeks ago by Bogdan1000
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Comment: C: computing resources for scRNA-seq analysis
... thank you for sharing your experience, i remember the step : samples.combined.list.anchors <- FindIntegrationAnchors(object.list = samples.combined.list, dims = 1:20) samples.combined.list.combined <- IntegrateData(anchorset = samples.combined.list.anchors, dims = 1:20) when th ...
written 7 weeks ago by Bogdan1000
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Comment: C: computing resources for scRNA-seq analysis
... yes, thank you for asking for more details. we typically use CellRanger on a SLURM cluster, and we have lots of resources there. after we obtain the matrices of counts for all the samples, in order to prototype the scRNAseq pipeline, i have been using my Ubuntu station (that has 64GB RAM). The pip ...
written 7 weeks ago by Bogdan1000
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Comment: C: computing resources for scRNA-seq analysis
... tthank you very much, Igor, for sharing your experience in the scRNAseq pipelines :) ...
written 7 weeks ago by Bogdan1000
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computing resources for scRNA-seq analysis
... Dear all, i would like for your suggestions please about the computing resources needed for scRNA-seq analysis running on 12 (or more) samples (each sample has 5000 - 6000 cells); we could use Seurat, Liger, Harmony, or SimpleSingleCell pipelines ; what would be the minimum RAM needed (having 64GB ...
scrna-seq R sequencing written 8 weeks ago by Bogdan1000
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Comment: C: about batch correction in scRNA-seq
... Hi Igor, thank you for your note. Very helpful, as they have pointed into the correct direction, many thanks ! Regarding the alignment of cells, we evaluate it mainly by the visual examination of TSNE or UMAP plots, and by the number of cells from different samples in each cluster (ie. the ratio). ...
written 4 months ago by Bogdan1000
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Answer: A: about batch correction in scRNA-seq
... Dear all, thank you all for your suggestions ! if I may ask for another suggestion please regarding scRNA-seq analysis: shall we have 2 scRNA-seq samples that do not align too well by using either CCA (in Seurat 2) or Seurat 3 methods (with batch correction in Harmony, Liger, Conos, etc, as we ha ...
written 4 months ago by Bogdan1000
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Answer: A: minimal free energy and RNA folding
... Dear all, many thanks for your time, replies, comments, and suggestions ! Stay healthy, and be safe ;) ! If I may add a question though : some of my colleagues are asking about the measures of the complexity of RNA secondary structures (that may take into consideration the number of hairpins, stem ...
written 4 months ago by Bogdan1000

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Popular Question 4 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 4 months ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
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Popular Question 4 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Scholar 5 months ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters
Popular Question 6 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 6 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
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