User: Bogdan

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Bogdan490
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490
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Trusted
Location:
Palo Alto, CA, USA
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Last seen:
4 weeks, 1 day ago
Joined:
10 years, 9 months ago
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Posts by Bogdan

<prev • 257 results • page 1 of 26 • next >
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Comment: C: filtering a VCF file based on genotype
... Thank you very much Valerie ! great to hear from you ... ...
written 4 weeks ago by Bogdan490
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filtering a VCF file based on genotype
... Dear all, I would appreciate having a piece of advice : shall we use the VariantAnnotation package, how shall I filter a VCF file in order to exclude the GERMLINE and TUMOR samples that have a GENOTYPE of "./". for example, if we aim to see the GENOTYPES in the vcf file, we receive the following m ...
variantannotation written 5 weeks ago by Bogdan490 • updated 4 weeks ago by Valerie Obenchain ♦♦ 6.5k
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Comment: C: VariantAnnotation and filtering a VCF
... I think I found the cause of the error : some Genotype GT fields were "." (i.e. NA) in the vcf file. ...
written 6 weeks ago by Bogdan490
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VariantAnnotation and filtering a VCF
... Dear Valerie, and all, i would appreciate a piece of help about filtering with VariantAnnotation, as i am getting the following message for some vcf files "Error: logical subscript contains NAs ". I am starting with a VCF file from DELLY that contains inversions, and I am setting up the code in th ...
variantannotation written 6 weeks ago by Bogdan490
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Comment: C: counting the sequencing reads in 10kb regions on a genome-wide scale
... Thank you James ! ...
written 3 months ago by Bogdan490
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counting the sequencing reads in 10kb regions on a genome-wide scale
... Dear all, during a step of a CNV analysis on cancer genomes, I would like to be able to COUNT and DISPLAY along the CHROMOSOME AXIS the NUMBER of READS in 10KB REGIONS of GERMLINE and CANCER GENOMES. I would like to ask you please for your suggestions about : -- any fast function/algorithm in R t ...
rsamtools cnv read counting written 3 months ago by Bogdan490 • updated 3 months ago by James W. MacDonald46k
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visualize CNV data based on WGS
... Dear all, we have been calling CNV (copy-number variations) in cancer genomes based on whole-genome sequencing data (WGS), using some of the packages available in BioC. Please would you advise -- what would be the best way to visualize WGS in order inspect visually the CNV predictions ? Is there ...
cnv written 5 months ago by Bogdan490
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Comment: C: normalization of CHIP-seq samples (ChIP and INPUT)
... Thank you. just found the answer : https://support.bioconductor.org/p/77193/ ...
written 6 months ago by Bogdan490
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Comment: C: normalization of CHIP-seq samples (ChIP and INPUT)
... Dear Aaron, great to hear from you, and thank you for suggestions. On a side note, thought I shall ask (following some old postings) : can we obtain the normalized counts by using also CPM function (below). Many thanks ! libSizes <- as.vector(colSums(x)) y <- DGEList(counts=x, group=grou ...
written 6 months ago by Bogdan490
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Comment: C: normalization of CHIP-seq samples (ChIP and INPUT)
... Dear Ryan, thank you for your reply. Here the question is not very much about TMM normalization (implemented in csaw or edgeR); I would be interested to know  whether I could normalize in the same procedure both ChIP samples and INPUT_DNA samples. Sorry if I missed the discussion in the manual. Any ...
written 6 months ago by Bogdan490

Latest awards to Bogdan

Popular Question 11 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 11 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 11 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 12 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 16 months ago, created a question with more than 1,000 views. For gene symbols in Gviz
Supporter 16 months ago, voted at least 25 times.
Centurion 2.4 years ago, created 100 posts.

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