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• How to generate the map file for selscan?
  Hello I have 2 datasets and want to analysis the XPEHH scores by selscan. I used plink and beag...
• XPEHH output file blank in SELSCAN
  I make a SELSCAN input file as .vcf file and a .map file with two population for XPEHH calculatio...
• Affy Axiom array - many cases of two probe set IDs sharing the same Affy SNP ID and dbSNP RS ID values. What's going on?
  Hello, I recently got back some genotyping data back from the core lab from the Axiom Human Orgi...
• Best tool for Fst calculation with over a thousand SNP among 6 populations??
  Hello, What tools are you guys using to calculate Fst? I tried Arlequin, Genalex etc. They all...
• Down-sample to one read per SNP loci per sample
  Does anyone know if there is a way of downsampling to a coverage of 1x per sample at known SNP lo...
• HIgh Fst outliers in lositan
  Hi, I'm running lositan on GBS data in two populations. Overall Fst is high between the populati...
• Different position of the same alternative locus
  Where do people get the position of GRCh38 alternative loci? I've found multiple sources, and th...
• Detecting selection with 'selscan' - How can I generate the correct input files from a phased VCF?
  I have a set of phased (Beagle) SNPs for one chromosome in VCF format and would like to use selsc...
• pick one sequence per locus
  I have a .loci archive with 1953 loci and 24 individuals. I need to extract only one sequence pe...
• Identity-By-Descent Used To Narrow Down Targets From Exome Sequencing Data
  I know someone will apply IBD or linkage analysis to further narrow down the variant targets from...
• Star alignment - AS and MD tags
  Hi, I am trying to understand some details about alignment of sequencing reads and the alignment...
• Help With Snp Array
  Dear all, First time to touch SNP array. I have a set of SNP array downloaded from TCGA. Now I a...
• How to identify the loci producing differential small RNAs between two samples?
  Hi, everyone, I have small RNA-seq data avaliable for two samples (wt and mutant), each of which...
• How to merge 2 alignment files with their partitions
  Hi all ---------- I am trying to create a tree from two alignment files. each alignment file ha...
• How to interpret XPEHH (recent selection) score?
  I have calculated XP-EHH and iHS scores for a set of snps using selscan. XP-EHH ranges from -0.75...
• how to find different gene loci between two strains
  I already have two complete genome,I want compare them to find different gene loci and related pr...
• Multiple-Sequence Alignment Trimming
  I want to construct a phylogenetic tree based on 5 housekeeping loci from two different Vibrio sp...
• Multiple Ensembl gene IDs for the same gene symbol (not haplotypic regions)
  Hi all, I have noticed something odd about the Mus musculus Ensembl annotation I'm currently usi...
• Extracting loci index from uniprot with high confidence
  I'm in the process of automating an assembly of paired multiple sequence alignments (i.e. MSAs wi...
• The reason two identical sequences have different accession numbers and different loci
   I am currently working on a certain gene.  I was looking for it in pigs among other species. In ...
• strange He vs Fst plot from Lositan
  I'm working with a panel of 13K SNPs generated using a modified ddRAD library prep. The two "popu...
• Loci identification through SNPs LD information
  Dear all, I want to define several loci in a genetic region through linkage disequilibrium inform...
• mapping reads to repetitive elements in genome?
  I have some ChIP-seq reads that mark repetitive elements (H3K9me3) in my genome. My data shows en...