User: Floris Brenk

gravatar for Floris Brenk
Floris Brenk970
Reputation:
970
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Location:
USA
Last seen:
1 week, 1 day ago
Joined:
6 years, 11 months ago
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about me

Posts by Floris Brenk

<prev • 181 results • page 1 of 19 • next >
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Calculating simple allele specific expression for certain variants
... Hi all, I have a couple perhaps somewhat naive questions about allele specific expression and was hoping that someone could push me in the right direction. We have a blood based RNAseq dataset and some samples have a clear pathogenic variant in them. One hypothesis is that of course if the damagin ...
ase allele specific expression rna-seq written 12 weeks ago by Floris Brenk970
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Answer: A: Covariates for eQTL analysis
... Dont think there is a golden standard approach here, much will depend on what you research question is? Couple things you can do: 1) impute your clinical data to fill in the NA 2) make PC's from your RNAseq data and check for correlation between these PC's and any of your clinical covariates 3) s ...
written 5 months ago by Floris Brenk970
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BAF and L2R Illumina vs Affymetrix
... Hi all, Was wondering if there any noteworthy differences between Illumina genotyping array and Affymetrix genotyping array (mainly UKB data) BAF and L2R values? or can they be interpret in an identical way? thanks! ...
baf l2r cnv written 5 months ago by Floris Brenk970
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Comment: C: Sizes of Nanopore files and how to store?
... Great thanks a lot Wouter, much appreciated! Think we will just delete the fast5 files which will save a lot of storage costs ...
written 7 months ago by Floris Brenk970
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Sizes of Nanopore files and how to store?
... Hi all, Had some practical questions about the output of the Nanopore PromethION and was hoping someone could help out. - What is the estimate size per flow-cell, best I could find is ranging from 2TB-3TB? - When using human DNA best I could find was that this was ~40X coverage, is this c ...
wgs nanopore long-read written 7 months ago by Floris Brenk970 • updated 7 months ago by WouterDeCoster44k
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chromosome X and Y GWAS results
... Dear all, I was wondering whether anyone knows of any robust GWAS loci on chromosome X and Y? Have been looking around a bit but haven't found much yet. Specifically curious whether there are differences in risk between male and females with risk variants are present on X. Thanks all! ...
gwas X Y written 11 months ago by Floris Brenk970
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Epistasis in GWAS loci, examples?
... Hi all, I was been working on epistasis in a couple of GWAS loci. Basically the theory is that some GWAS loci might not work in an additive manner, but more in an epistasic way and calculated this using R : Formula <- formula(paste("pheno ~ PC1 + PC2 + PC3 + PC4 + PC5 + SEX + SNP1 * SNP2")) ...
epistasis gwas R written 21 months ago by Floris Brenk970
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Rare variant meta-analyzing tests
... Hi all, I have 5 different (dosage VCF files, with both continuous and binary phenotypes) datasets and I'm trying to meta-analyze rare variants in each dataset. Ideally I would like to group the variants per gene and then meta-analyze the p-values per gene from all 5 datasets, but I haven't found a ...
meta analyze rare variants written 2.8 years ago by Floris Brenk970 • updated 18 months ago by swetansu0
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Add gene annotation/information to CNV plot in R
... Hi all, Im have a few interesting (genotyping) CNVs and now I want to plot them using the B allele frequency and LogR ratio. There are already several topics about this [for example here][1], but ideally I am more looking for something like pennCNV plots but then with gene annotation on the x-axis ...
R cnv plot written 3.0 years ago by Floris Brenk970 • updated 3.0 years ago by cmdcolin1.4k
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Comment: C: ATACseq and HiC sequencing
... Great thanks all for your help, much appreciated! Got one more additional questions, is there any need to PhiX spike-in during HiC or ATAC sequencing? or can the libraries just go on hiseq without issues? ...
written 3.1 years ago by Floris Brenk970

Latest awards to Floris Brenk

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: PCA using HapMap population data
Great Question 9 weeks ago, created a question with more than 5,000 views. For Reformat minimac imputated files to plink file
Popular Question 4 months ago, created a question with more than 1,000 views. For Covariates... what to do with them and how to handle them?
Guru 4 months ago, received more than 100 upvotes.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Population stratification in targeted sequencing?
Scholar 5 months ago, created an answer that has been accepted. For A: Assigning haplotypes to individuals
Popular Question 11 months ago, created a question with more than 1,000 views. For Coverage/Read Depth per SNP in 1000Genomes
Popular Question 18 months ago, created a question with more than 1,000 views. For RNA-seq de novo transcript assembly from one gene
Popular Question 18 months ago, created a question with more than 1,000 views. For creating chr17 haplotypes h1 and h2 from exome / gwas data
Popular Question 18 months ago, created a question with more than 1,000 views. For Covariates... what to do with them and how to handle them?
Scholar 18 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Popular Question 18 months ago, created a question with more than 1,000 views. For Assigning haplotypes to individuals
Popular Question 20 months ago, created a question with more than 1,000 views. For Covariates... what to do with them and how to handle them?
Popular Question 20 months ago, created a question with more than 1,000 views. For Assigning haplotypes to individuals
Student 20 months ago, asked a question with at least 3 up-votes. For Imputation of chromosome X using the Michigan imputation server
Popular Question 20 months ago, created a question with more than 1,000 views. For RNA-seq de novo transcript assembly from one gene
Popular Question 21 months ago, created a question with more than 1,000 views. For Looking for a whole genome sequencing analysis course
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Pre-calculated Ka/Ks ratio per gene of human genome
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Conservation score for a piece of human genome
Popular Question 2.2 years ago, created a question with more than 1,000 views. For creating chr17 haplotypes h1 and h2 from exome / gwas data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Covariates... what to do with them and how to handle them?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Looking for a whole genome sequencing analysis course
Great Question 2.2 years ago, created a question with more than 5,000 views. For r2 correlation interpretation snp in plink pruning
Great Question 2.2 years ago, created a question with more than 5,000 views. For Reformat minimac imputated files to plink file

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