User: Bogdan

gravatar for Bogdan
Bogdan800
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800
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Location:
Palo Alto, CA, USA
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Google Scholar Page
Last seen:
2 weeks, 5 days ago
Joined:
7 years ago
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about me

Posts by Bogdan

<prev • 237 results • page 1 of 24 • next >
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about GWAS studies and causal variants
... Dear all, thought that i could ask you please : from a series of Genome Wide Association Studies, we can see some variants that are associated with an ocular disease, that are LoF (Loss of function) or PVT (trigger protein truncations). what is the chance of these LoF or PVT variants to be causa ...
gwas snp written 5 weeks ago by Bogdan800 • updated 5 weeks ago by WouterDeCoster40k
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Answer: A: Single Cell RNA Seq. Analysis
... Yes, Seurat would be one of the starting points. Beside the tutorials offered on Seurat web site, a while I have posted some R code on Seurat github page : https://github.com/satijalab/seurat/issues/1193 (hope it is helpful) ...
written 3 months ago by Bogdan800
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Comment: A: TPM values of expressed genes
... Thank you very much for your comments and insights ;) ...
written 4 months ago by Bogdan800
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TPM values of expressed genes
... Dear all, considering a RNA-seq experiment and analysis that provides the expression values as TPM, please would you let me know what is a minimum TPM value in order to consider a gene to be expressed ? talking about RPKM.FPKM units, I remember that a gene was considered expressed if RPKM (or FPK ...
rna-seq written 4 months ago by Bogdan800 • updated 4 months ago by i.sudbery5.0k
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Answer: A: a webserver for the bigwig files
... Thank you. Yes, the answer from UCSC folks was : "There are a few different public options you can use to host your big* data. A number of our users utilize CyVerse (http://www.cyverse.org/), but I encourage you to look at our FAQ page on the topic and explore all the options (https://genome.ucsc. ...
written 4 months ago by Bogdan800
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Comment: C: a webserver for the bigwig files
... thanks, yes, a Google Cloud bucket will help. Just came across a description on ENCODE page : https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/tutorial_google.md ...
written 5 months ago by Bogdan800
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Comment: C: a webserver for the bigwig files
... yes, thank you, what cloud service would you recommend ? ...
written 5 months ago by Bogdan800
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a webserver for the bigwig files
... Dear all, would you please advise : which (public) webserver would you recommend to host the bigwig files, in order to upload the tracks in the UCSC browser ? thank you very much, -- bogdan ...
bigwig written 5 months ago by Bogdan800
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Comment: C: gene counts in Seurat after RunCCA() and AlignSubspace()
... Thank you, Igor. If I may add please a follow up question : for batch correction in scRNA-seq (when comparing multiple cell treatments), which algorithm would you recommend ? mnnCorrect() in SCRAN, combat() in SVA, or any other algorithm ? thanks a lot ! ...
written 6 months ago by Bogdan800
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Comment: C: gene counts in Seurat after RunCCA() and AlignSubspace()
... Thanks a lot, Avi. Yes, it is very helpful indeed. After extracting the NORM.DATA and SCALE.DATA for a few cells in the original matrix, and comparing the expression values at different steps in the algorithm : -- indeed I have not seen any changes in the numerical values in @DATA (there is no bat ...
written 6 months ago by Bogdan800

Latest awards to Bogdan

Popular Question 25 days ago, created a question with more than 1,000 views. For filtering VCF files
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For annotation of SV (structural variants)
Popular Question 3 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 3 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Student 3 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Student 3 months ago, asked a question with at least 3 up-votes. For intersect VCF files
Popular Question 3 months ago, created a question with more than 1,000 views. For filtering VCF files
Scholar 3 months ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters
Great Question 4 months ago, created a question with more than 5,000 views. For intersect VCF files
Appreciated 6 months ago, created a post with more than 5 votes. For annotation of SV (structural variants)
Popular Question 6 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 6 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 7 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 7 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 7 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 7 months ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
Popular Question 8 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 8 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 8 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 10 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 10 months ago, created a question with more than 1,000 views. For filtering VCF files
Appreciated 10 months ago, created a post with more than 5 votes. For sharing BiocWorkshops 2018
Popular Question 10 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 11 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 12 months ago, created a question with more than 1,000 views. For filtering VCF files

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