User: Bogdan

gravatar for Bogdan
Bogdan260
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260
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Location:
Palo Alto, CA, USA
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2 weeks, 6 days ago
Joined:
5 years, 2 months ago
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Posts by Bogdan

<prev • 112 results • page 1 of 12 • next >
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normalization of POL2 ChIP-seq for the calculation of POL2 Pausing Ratios
... Dear all, please could you advise about a way (ie a package/function in BioC) to normalize the ChIP-seq data for the calculation of POLYMERASE2 PAUSING RATIO (PR) for all the genes in the genome ; we have a POL2 ChIP-seq dataset, and we compute the PAUSING RATIO (PR) as the ratio between the regio ...
deseq2 chip-seq edger written 23 days ago by Bogdan260
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Answer: A: calling the CNV in tumor-only samples (WGS and WES)
... Thanks, Eric. will write to you as soon as i have a free minute; essentially CNVkit did run on our samples, although i would have to talk with you about the output. Thanks again ! ...
written 5 weeks ago by Bogdan260
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Comment: C: calling the CNV in tumor-only samples (WGS and WES)
... Dear Eric, great to hear from you ;) if it is OK by you, will get back to you by email, as we have a few questions about CNVkit ;). ...
written 6 weeks ago by Bogdan260
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calling the CNV in tumor-only samples (WGS and WES)
... Dear all, please, which algorithm(s) would you recommend for calling the CNV in tumor-only samples (obtained by either WES or WGS technology ? I would gladly use GATK4, although hmmm ... we do not have so many samples in order to generate a PoN (a panel of normals). many thanks, bogdan ...
cnv written 6 weeks ago by Bogdan260
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Comment: C: extracting Allele Read Counts
... thank you for your suggestions ;) ...
written 6 weeks ago by Bogdan260
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Answer: A: Loss of heterozygosity analysis from SNV files
... I think that the regions of LOH are labelled as ""SS=3" in the vcf file from VARSCAN. ...
written 7 weeks ago by Bogdan260
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Comment: C: WES or WGS analysis of cancer samples with no matched germline
... Thanks Marcus ! thanks, it is working in GATK 3.8. ...
written 9 weeks ago by Bogdan260
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Comment: C: WES or WGS analysis of cancer samples with no matched germline
... Dear Marcus, thank a lot for your suggestions. Yes, we have been using MUTECT2 and cn.MOPS for detecting SNV and CNV in germline-tumor pairs. However, when we have only a TUMOR sample (with no GERMLINE sequence), may I ask, how would you run MUTECT2 ? ...
written 9 weeks ago by Bogdan260
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Comment: C: WES or WGS analysis of cancer samples with no matched germline
... Hi Wouter, thanks : we aim to identify the SNV and CNV in the tumor samples (and some of these samples do not have a matched normal sample). ...
written 9 weeks ago by Bogdan260
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WES or WGS analysis of cancer samples with no matched germline
... Dear all, although this question has been asked before (~ 2 years ago), if I may ask it again, as I am looking for some updated workflows, strategies, ideas : "what would be the acceptable pipeline for processing WES or WGS data from primary tumors that do not have matched germlines sequences ?" ...
wgs wes snv cnv written 9 weeks ago by Bogdan260 • updated 9 weeks ago by markus.riester210

Latest awards to Bogdan

Popular Question 9 weeks ago, created a question with more than 1,000 views. For intersect VCF files
Popular Question 3 months ago, created a question with more than 1,000 views. For about xlim() in ggbio and CIRCLE layout
Centurion 5 months ago, created 100 posts.
Student 5 months ago, asked a question with at least 3 up-votes. For annotation of SV (Structural Variants)
Supporter 6 months ago, voted at least 25 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For about GRAnges and append
Scholar 17 months ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters

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