User: Bogdan

gravatar for Bogdan
Bogdan420
Reputation:
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Trusted
Location:
Palo Alto, CA, USA
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Last seen:
2 days, 3 hours ago
Joined:
5 years, 7 months ago
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about me

Posts by Bogdan

<prev • 166 results • page 1 of 17 • next >
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Comment: C: annotation of SV (structural variants)
... Dear Daniel, thank you. May I add and ask : how is a TRA 3to5 different than a TRA 5to3 ? thank you ;) ! ...
written 2 days ago by Bogdan420
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Comment: C: annotation of SV (structural variants)
... Dear Daniel, talking about TRUNCATIONS, shall we define the gene TRUNCATIONS, based on your R code that is available at https://github.com/PapenfussLab/gridss/blob/master/example/somatic-fusion-gene-candidates.R, I believe that we only have to change the lines 70-72 of the R code by "negation" of ...
written 3 days ago by Bogdan420
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Comment: C: annotation of SV (structural variants)
... And talking about INV, yes, thank you, I am very happy that your R package reports annotations for both 5to5 ad 3to3 INV breakpoints ;) ...
written 3 days ago by Bogdan420
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Comment: C: annotation of SV (structural variants)
... Dear Daniel, thanks a lot ! we wish you a happy and fruitful week ! If I may add a question, this time if about TRA, specifically about 3to5, and 5to3 TRANSLOCATIONS. When do we define a TRA as 3to5, and when it is a TRA 5to3 ? I believe that these are RECIPROCAL TRA. thank you ! ...
written 3 days ago by Bogdan420
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4C interaction analysis
... Dear all, please would you let me know, would you have a recommendation regarding the algorithm to use for 4C data analysis (we do not have replicates). A few analysis algorithms are listed here on omictools.com : https://omictools.com/4c-analysis-category thank you ! -- bogdan ...
4c written 3 days ago by Bogdan420
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Comment: C: annotation of SV (structural variants)
... And, if I may add please another question (that is a bit naive as I have not checked the answer yet): depending on the type of SV and depending on the type of SV direction/orientation (3to5, 5to3, 5to5, 3tot3), shall we refer to INVERSIONS, would we need to include in the R script that computes ...
written 7 days ago by Bogdan420
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Comment: C: annotation of SV (structural variants)
... Dear Daniel, thank you. We have used DELLY and LUMPY, and now i am looking also into GRIDSS, as our friends from Stanford were very very excited about using GRIDSS on calling SV in cancer genomes. ...
written 7 days ago by Bogdan420
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Comment: C: annotation of SV (structural variants)
... Dear Daniel, thank you for your reply. Please if I may add a note below, as I would like to understand much better how the "+" and "-" are assigned please : we have been using DELLY on a few cancer genomes that we had, and DELLY gives the following SV: DEL are always 3to5 DUP are always 5to3 ...
written 7 days ago by Bogdan420
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Comment: C: annotation of SV (structural variants)
... I have tried SnpEff with an output vcf file from DELLY 0.7.5, where the TRANSLOCATIONS are annotated in format, and not in format, and the latest version of SnpEff did not wok on items. ...
written 10 days ago by Bogdan420
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Comment: C: about somatic mutation calling
... Hi Chirag, for filtering, you can use please VCFTOOLS or VCFLIB . Talking about the tiers 1 to 5, we could ask the author of the algorithm. ...
written 11 days ago by Bogdan420

Latest awards to Bogdan

Popular Question 7 days ago, created a question with more than 1,000 views. For about merging VCF files
Student 11 days ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 20 days ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 10 weeks ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 3 months ago, created a question with more than 1,000 views. For about merging VCF files
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to analyze RIP-seq data
Student 3 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 5 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 7 months ago, created a question with more than 1,000 views. For intersect VCF files
Popular Question 8 months ago, created a question with more than 1,000 views. For about xlim() in ggbio and CIRCLE layout
Centurion 10 months ago, created 100 posts.
Student 10 months ago, asked a question with at least 3 up-votes. For annotation of SV (Structural Variants)
Supporter 11 months ago, voted at least 25 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For about GRAnges and append
Scholar 22 months ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters

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