User: Bogdan

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Bogdan720
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Palo Alto, CA, USA
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Posts by Bogdan

<prev • 235 results • page 1 of 24 • next >
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Comment: A: TPM values of expressed genes
... Thank you very much for your comments and insights ;) ...
written 18 days ago by Bogdan720
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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 19 days ago by Bogdan720 • updated 17 days ago by i.sudbery4.1k
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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 23 days ago by Bogdan720
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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 29 days ago by Bogdan720
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Comment: C: a webserver for the bigwig files
... yes, thank you, what cloud service would you recommend ? ...
written 29 days ago by Bogdan720
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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 29 days ago by Bogdan720
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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 9 weeks ago by Bogdan720
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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 9 weeks ago by Bogdan720
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Answer: A: 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 ba ...
written 9 weeks ago by Bogdan720
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Comment: C: gene counts in Seurat after RunCCA() and AlignSubspace()
... Thank you Igor .. oh well, as I am not a statistician, my thought was that AlignSubspace() function provides also "corrected" counts, as mnnCorrect() or Combat() would do. however, I can see that RunCCA() change the expression values in the @scale.data for some cells : if I may ask, how does it do ...
written 9 weeks ago by Bogdan720

Latest awards to Bogdan

Appreciated 8 weeks ago, created a post with more than 5 votes. For annotation of SV (structural variants)
Popular Question 10 weeks ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 10 weeks ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
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
Popular Question 3 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 3 months ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
Popular Question 4 months ago, created a question with more than 1,000 views. For filtering VCF files
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 filtering VCF files
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 filtering VCF files
Appreciated 6 months ago, created a post with more than 5 votes. For sharing BiocWorkshops 2018
Popular Question 6 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 filtering VCF files
Popular Question 8 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 about merging VCF files
Popular Question 12 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 12 months ago, created a question with more than 1,000 views. For "for loop" and AUTOPLOT function
Popular Question 12 months ago, created a question with more than 1,000 views. For estimating tumor purity and ploidy and CNV
Popular Question 12 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 13 months ago, created a question with more than 1,000 views. For about merging VCF files
Student 13 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 13 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 15 months ago, created a question with more than 1,000 views. For about merging VCF files

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