User: Ryan D

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Ryan D3.3k
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http://twitter.com/#!/...
Last seen:
4 years, 1 month ago
Joined:
8 years, 3 months ago
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r*************@vanderbilt.edu

Twitter: @delahar
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Posts by Ryan D

<prev • 175 results • page 1 of 18 • next >
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Comment: C: Comparing CNAs from two groups
... Just curious if your CNAs all have identical breakpoints or not. What is the minor allele frequency threshold you are using? We typically examine only those CNVs with 5% MAF or higher. ...
written 4.3 years ago by Ryan D3.3k
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Comment: C: PLINK returns NA values for all minor allele frequencies in my data
... Did you check your plink.hh file? It says you have a lot of haploid genotypes present. This suggests that your file format might be off. ...
written 4.3 years ago by Ryan D3.3k
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Renaming SNPs or SNP matching
... This should be easy to do by now, but... we have SNP data from an Illumina exome array given to us in PLINK format. The BIM file looks like this: 1 exm2253575 0 881627 G A 1 exm269 0 881918 A G 1 exm340 0 888659 T C 1 exm348 0 ...
vcf bedtools exome-chip bim snp written 4.3 years ago by Ryan D3.3k • updated 2.3 years ago by vakul.mohanty240
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Comment: C: What Is The Importance Of The Hardy Weinberg Equilibrium In Gwas?
... I would say yes, if several SNPs are in high LD (say r2>0.8 or 0.9) and all out of HWE, you can typically assume it is a legitimate association. The chance of having 3 or more SNPs in high LD fail HWE checks because they all genotype badly is pretty low. The only other way this could happen--that ...
written 4.4 years ago by Ryan D3.3k
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Comment: C: Easiest way to determine copy number for all SVs in all samples in 1000 Genomes
... Not an answer to the question, but ostensibly the most recent phase3 release does have copy number declarations in it: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ . That information comes from Laura Clarke with the 1000 Genomes Project. Ryan ...
written 4.5 years ago by Ryan D3.3k
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Easiest way to determine copy number for all SVs in all samples in 1000 Genomes
... Hello Biostars, I was wondering if there is a PLINK file available that has the copy number status of all structural variants (SVs) for samples in the 1000 Genomes. I know they are often named with names such as MERGED_DEL_2_106009 which is the same as esv2666691 in the UCSC genome browser. What I ...
sv 1000 genomes structural-variants plink cnv written 4.5 years ago by Ryan D3.3k • updated 4.4 years ago by Biostar ♦♦ 20
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Comment: C: How To Get Full Information About Rna-Seq File?
... Some better tags might be useful above. "How", "to", "get" etc. are not useful. ...
written 4.8 years ago by Ryan D3.3k
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Answer: A: Cnv Data
... This is a place that really suffers in the TCGA annotation. The file handles are different from the TCGA IDs and so you have to map each "barcode" back to the TCGA ID and determine if it is tumor/normal etc. I think that information comes as part of the download through the TCGA portal mentioned abo ...
written 4.8 years ago by Ryan D3.3k
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Answer: A: Tools For Analyzing Copy Number Variation On All-Tumor Exome-Seq Samples
... A group here has had a great deal of success in using Varscan2 and ExomCNV due to the non-uniform nature of exon coverage across the genome. See the paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759720/ , though XHMM has worked fairly well for us if you have a number of samples run under the ...
written 4.8 years ago by Ryan D3.3k
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Comment: C: Cnv Annotation Tools
... I would add for the "known CNVs" that we use those as discovered by 1000 Genomes but other files such as the DGV can also be used. ...
written 4.8 years ago by Ryan D3.3k

Latest awards to Ryan D

Popular Question 4.1 years ago, created a question with more than 1,000 views. For Largest (Publicly) Available Gwas Datasets
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Largest (Publicly) Available Gwas Datasets
Good Answer 4.2 years ago, created an answer that was upvoted at least 5 times. For A: 1000 Genomes Ld Calculation
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Resequencing Genes/Regions Identified By Gwas
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Using Tabix And Vcf Tools To Get Cnv / Sv Frequencies From 1000 Genomes Data
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Using Tabix And Vcf Tools To Get Cnv / Sv Frequencies From 1000 Genomes Data
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Exome Sequencing Depth/Target Considerations And Shared Controls
Epic Question 4.4 years ago, created a question with more than 10,000 views. For 1000 Genomes Ld Calculation
Appreciated 4.6 years ago, created a post with more than 5 votes. For Investigating Synthetic Associations
Scholar 4.6 years ago, created an answer that has been accepted. For A: Cnv Annotation Tools
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Calculate Ld Between 2 Loci
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Strand-Orientation In Meta-Analysis With Plink
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Using Tabix And Vcf Tools To Get Cnv / Sv Frequencies From 1000 Genomes Data
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Distributing And Tracking Work Among Bioinformaticians
Prophet 4.7 years ago, created a post with more than 20 followers. For Tool To Generate Proportional Venn Diagrams?
Appreciated 4.8 years ago, created a post with more than 5 votes. For Linking Mirnas With Disease Or Keywords
Appreciated 4.8 years ago, created a post with more than 5 votes. For Merging And Binning Genomic Segments
Appreciated 4.8 years ago, created a post with more than 5 votes. For 1000 Genomes Ld Calculation
Appreciated 4.8 years ago, created a post with more than 5 votes. For How Connected Are Researchers In Pubmed?
Appreciated 4.8 years ago, created a post with more than 5 votes. For Resequencing Genes/Regions Identified By Gwas
Appreciated 4.8 years ago, created a post with more than 5 votes. For Imputation Improvement From Hapmap To 1000 Genomes
Appreciated 4.8 years ago, created a post with more than 5 votes. For Determining Which New Snps In 1000G Data Result In Coding Changes
Appreciated 4.8 years ago, created a post with more than 5 votes. For Tool To Generate Proportional Venn Diagrams?

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