User: Bogdan

gravatar for Bogdan
Bogdan300
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300
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Trusted
Location:
Palo Alto, CA, USA
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Last seen:
3 weeks, 3 days ago
Joined:
5 years, 4 months ago
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Posts by Bogdan

<prev • 117 results • page 1 of 12 • next >
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Comment: C: normalization of POL2 ChIP-seq for the calculation of POL2 Pausing Ratios
... Thank you very much, Carlo ;) ...
written 24 days ago by Bogdan300
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Comment: C: extracting the exons coordinates on hg38
... Dear gentlemen, thank you for your replies : very much appreciate your help ;). Yes, i knew the previous postings related to extracting the hg19 exon coordinates before i emailed ; although it applies a bit differently to hg38 and to RefSeq genes. I thought that we may find 2 solutions to the sam ...
written 6 weeks ago by Bogdan300
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extracting the exons coordinates on hg38
... Dear all, please could you advise : how can we obtain the coordinates of exons of the RefSeq or UCSC genes (canonical isoforms) on hg38, where each coordinates (chr, start, end) also have assigned the gene name .. ? thanks a lot, and a happy weekend, -- bogdan ...
genome exome written 6 weeks ago by Bogdan300 • updated 6 weeks ago by chen1.2k
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Comment: C: CNV calling on tumor sample with no germline counterpart
... thank you Eric, it is very informative ;) ...
written 7 weeks ago by Bogdan300
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CNV calling on tumor sample with no germline counterpart
... Dear all, please would you recommend the algorithms/software that perform CNV calling on WGS data of TUMOR sample with NO GERMLINE counterpart ? Many thanks, -- bogdan ...
cnv written 7 weeks ago by Bogdan300 • updated 7 weeks ago by Eric T.1.9k
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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 12 weeks ago by Bogdan300 • updated 24 days ago by Carlo Yague3.3k
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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 3 months ago by Bogdan300
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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 3 months ago by Bogdan300
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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 3 months ago by Bogdan300
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Comment: C: extracting Allele Read Counts
... thank you for your suggestions ;) ...
written 3 months ago by Bogdan300

Latest awards to Bogdan

Popular Question 12 weeks ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 4 months ago, created a question with more than 1,000 views. For intersect VCF files
Popular Question 5 months ago, created a question with more than 1,000 views. For about xlim() in ggbio and CIRCLE layout
Centurion 7 months ago, created 100 posts.
Student 7 months ago, asked a question with at least 3 up-votes. For annotation of SV (Structural Variants)
Supporter 9 months ago, voted at least 25 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For about GRAnges and append
Scholar 19 months ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters

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