More posts like this
-
Relatedness and GWAS False Signals
written by another_bioinformatician 0I have just realized that a GWAS that I ran sadly included related individuals (the flagged samples file that came with the dataset did not …
-
detection of signature selection using relative individuals
written by kk.mahsa 15Does detection of the signature of selection use relative individuals cause bias in the results?
-
Counting the number of major and minor alleles
written by kk.mahsa 15In a multi-sample VCF file, How can we count the number of major and minor alleles for an SNP in all samples? Should we use …
-
Use of GenotypeGVCFs in population genetic studies
written by kk.mahsa 15I have 16 whole genome sequenced samples from two populations (8 for each population). My goal is detection of signature of selection and introgression. I …
-
Assign gene signature in other cohort
written by sunnlife 0Hi, Via a GSE dataset, I identify a gene signature of hundred of genes specific to a particular class of samples. Now I want identify …
-
Protein Domain Characterization: Conflicting results from Interpro
written by venura 7Hi, When I was trying to characterize a set of proteins using Interpro, I came across the following scenario. One of the proteins there is …
-
Variant association analysis with both related and unrelated individuals
written by seta 191Dear all, I'm going to do an association analysis of a set of common SNPs with some binary and quantitative traits, encompassing both related and …
-
Chromosome X GWAS in related individuals
written by alesssia 58Dear all, I would like to include the X Chromosome in a GWAS of a continuous trait which has been measured in a dataset of …
-
Group/Cluster tumor samples in an RNA-Seq dataset for survival analysis, based on the expression of…
written by svlachavas 79Dear Community, based on a collaboration project, we have identified a small gene signature, discriminating relatively well control samples from tumor ones, based on an …
-
gene expression in disease and normal
written by rob.costa1234 32I am stuck with a problem that is more of a trouble shooting with basic understanding rather than using any software/ statistical package. I want …
It entirely depends on what method you are using.
I want to use Fst and XP-EHH. Which methods are suitable for samples similar to the ones mentioned above?