• Converting Genotype Data to Structure Input Format

    Hi, I have a text file with SNP data that I'd like to convert to an input file for Structure. Cur...

  • STRUCTURE software format

    Hello,

    I am using STRUCTURE 2.3.4 software for population genetic analysis. But something goes w...

  • SNP array data storage and management with RDBMS (postgres)

    In our current data set, we have phenotype data on nearly one million individuals; we store this ...

  • Generating Summary Statistics And Coverage Plots From Illumina Ga2 Data

    We have performed a targeted sequencing of a few megabases of human DNA on ~20 samples using Illu...

  • Collapse rows in a data.frame but add new column for multiple values

    I have a data.frame where I need to collapse rows by sample names in the indiv.ID column. Here is...

  • Phylogenetic Comparative Methods: PGLS

    Hey guys,
    I have a a 13 columns 58 row table, where each row is a species and each column represe...

  • How to normalize gene expression values for finding similar genes

    I am a bit confused on the kind of data transformation I have to use for analyzing gene expressio...

  • Bash: awk: Calculate average of first 10 rows in column?

    Hi all,

    I'm working with video data for drug phenotypes on some mutant cell lines. Output is th...

  • Calculating mutation significance of each location in a BED file.

    Hello,

    I have ~250 patient INDEL and SNV vcfs from ICGC on one side. On the other side, I have a...

  • converting genotype file to vcf

    hi,

    I have some data in the format

    113934 126070
    Individual1 0 0
    Individual1 0 0
    ...

  • Fst value inflation in BayeScan?

    I am testing several RADseq SNP datasets for Fst outliers using BayeScan 2.1. These datasets repr...

  • GWAS with more than two alleles per locus

    I am trying to find the genes responsible for trait variation in a yeast population. The populati...

  • PGDSpider command line can't find pop file?

    G'day all,

    I am trying to convert a vcf file to a genepop file using PGDSpider command line. I w...

  • SNP IDs changed when making .ped files using PLINK

    I have data on genetic variants for multiple individuals for a family in the form of a .vcf file....

  • InsideDNA: 5 Unix commands every bioinformatician should know

    Bioinformaticians often have to manage large text files containing reads, sequences of genomes, a...

  • Extracting Specific Columns from Multiple Files & Writing to File Python

    I am currently learning Python. I would really like you help to solve the following problem using...

  • How to get the average number of pairwise differences among populations?

    I have genetic data in .structure and .vcf format (and can easily reach other formats with [PGDSp...

  • GWAS analysis using PLINK

    I have a GenomeStudio genotype file with missing genotypes denoted by "-"

    Using this file I gene...

  • is there any statistical way to analysis two groups without replications?

    I have a data frame with several rows as gene names and 3 columns with gen-expression value for e...

  • selecting short regions with multiple SNPs to write to a fasta file using SNP data generated from short read data

    Hi,

    I am trying to do an analysis that requires sequence data, and not SNPs directly (Extended B...



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