User: anp375

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anp375150
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Posts by anp375

<prev • 72 results • page 1 of 8 • next >
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Statistical Genetics - What information is required for haplotype phasing in a novel, admixed population?
... Let's say there is a population that has never been sequenced before and has experienced varying levels of admixture from multiple sources at different times. There is ancient admixture and recent admixture. Also, the population is highly consanguineous, but also very genetically diverse and did not ...
exome haplotype admixture phasing written 11 months ago by anp375150
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Answer: A: p-adjusted value to find out DE genes.
... http://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html ...
written 15 months ago by anp375150
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Answer: A: Interpreting GSEA results
... Normally, IPA handles this. Was the data normalized? I'd say plot all the log2foldchanges for all genes, and then highlight the genes that were assigned to that pathway. ...
written 15 months ago by anp375150
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Answer: A: Beagle to plink
... I think BEAGLE does that: http://faculty.washington.edu/browning/beagle_utilities/utilities.html#beagle2vcf ...
written 15 months ago by anp375150
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Tool for Pathway Analysis on SKAT results
... Hi, I was wondering if there is a tool, or at least a clearly defined procedure, available that could perform pathway analysis on SKAT results and take advantage of the P-values and common/rare variant assignments. In the SKAT output, I have gene names, the number of rare variants assigned to each ...
skat exome dna-seq pathway analysis written 15 months ago by anp375150
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Comment: C: How can I remove Indels from a VCF file that are actually microsatellite variant
... Thank you. Hopefully I get the BAMs soon. ...
written 17 months ago by anp375150
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How can I remove Indels from a VCF file that are actually microsatellite variants?
... I don't have access to the BAM files that were used to generate the VCF. I only have the VCF file. How do I go through indels in the VCF file and remove sequence repeat variants? Thanks. ...
indel microsatellite written 17 months ago by anp375150 • updated 17 months ago by Pierre Lindenbaum118k
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Comment: C: What are the typical IBD PIHAT values calculated by PLINK for duplicate samples?
... I don't understand what cryptic relatedness has to do with this. Right now, I assume that the differences arise from how PLINK handled missing genotypes in the data and how indels were called differently in the two sequencing sets. ...
written 17 months ago by anp375150
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What are the typical IBD PIHAT values calculated by PLINK for duplicate samples?
... I want to check for concordance in two different sequencing datasets. One is whole exome sequencing and the other is whole genome sequencing. 6 samples were sequenced in both sets. The PLINK IBD calculation for the duplicate samples gives pairwise PIHAT values above 0.5 (first degree relatedness), ...
plink ibd written 17 months ago by anp375150 • updated 17 months ago by MAPK1.4k
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Comment: C: TruSeq Exome Enrichment Kit Targeted Regions BED File
... It may be late for this, but the bed file you supplied covers exactly the same amount of region as the nextera rapid capture expanded exome kit covers. They may be exactly the same. EDIT: They actually do cover the same regions - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-4 ...
written 18 months ago by anp375150

Latest awards to anp375

Popular Question 10 months ago, created a question with more than 1,000 views. For Ingenuity Pathway Analysis by Variant Density?
Popular Question 10 months ago, created a question with more than 1,000 views. For Genbank identifiers vs Entrez Gene ID?
Popular Question 10 months ago, created a question with more than 1,000 views. For GO descriptions not printing out
Popular Question 10 months ago, created a question with more than 1,000 views. For How do I get Genbank files by using wiki gene ids in bioperl?
Popular Question 13 months ago, created a question with more than 1,000 views. For GO descriptions not printing out
Scholar 14 months ago, created an answer that has been accepted. For A: p-adjusted value to find out DE genes.
Great Question 15 months ago, created a question with more than 5,000 views. For Genbank identifiers vs Entrez Gene ID?
Supporter 2.2 years ago, voted at least 25 times.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Genbank identifiers vs Entrez Gene ID?

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