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• FASTA FILE to TABLE R/python
  Hi all, Does anyone knows who to convert a DNA sequence from a fasta file to a table of one col...
• Logic To Get Consensus Sequence
  I have a set of aligned sequences in fasta format. I want to get consensus out of the alignment. ...
• Many 0 in ped file converted from vcf genomic data
  Hi everyone, I am learning do the gwas analysis. When I convert the genomic data "1001genomes_sn...
• Consensus Sequence
  Hello, I have below 8 sequences and I would like to calculate a consensus sequence from them. se...
• generating a reasonable consensus with bcftools + vcf-consensus
  Hi, I want to generate a consensus sequence using a bam alignment from a specific genome locati...
• merging plink files
  i have been trying to merge some ped/map files. i had removed or renamed the duplicated in the ma...
• What are lowercase a,t,c,g refer to in a complete genome? Should lower case a,t,c,g to be converted to uppercase A,T,C,G before simulation?
  Hello All, In the file complete genome file of fruit fly (GCF_000001215.4_Release_6_plus_ISO1_MT...
• Obtain heterozyous/IUPAC consensus sequences from multiple sequence alignment
  Hi all,   I wonder if anyone has tried out something to obtain a consensus sequence with IUPAC ...
• Is there a code to find consensus motif
  Hello, I've been trying to write a code to find a consensus motif in a given sequence, and for t...
• Extract consensus sequence reads (collapse PCR duplicates) from bam
  Hi, I did an experiment where I designed a sequencing library focused on a specific genomic regi...
• Convert Plink Ped Format Into Hapmap Format?
  Is there a way to convert from ped PLINK format into HapMap genotype format? I've got PED PLINK f...
• Case-Control Discrimination In .Ped File Of Plink
  Hi, I have two queries: 1) I have .ped file (mentioned below). Here, I have all columns require...
• Indel results of GATK is not correct
  Hi: I use GATK (reference is b37) to call snp & indel ,but I have some problems with the res...
• Sorting the haplotypes by similarities of SNPs in R
  I have a data set and I want to sort it in the following way in R. I hope I can explain clearly. ...
• What distance metric to use for clustering fragments of genes, like 16S rRNA, or DNA fragments?
  I am trying to apply different clustering algorithms on sequence data with lengths about 240-260....
• Regenotype vcf using some samples as reference
  I have a VCF file with 24 control samples and 24 treated sample all called jointly through GATK. ...
• Generate Consensus Sequence from Pairwise Alignment
  Hi All, I am aligning a consensus sequence with a reference genome by pairwise alignment. Is the...
• How to fetch those line having only similar characters.
  Hello friends, I have a file having multiple nucleotides present in a comma separated format. I w...
• How to merge VCF files for SNP's ?
  Hi all I called six SNP's files as individual, I want to merge them such that considering the po...
• How to handle gaps in consensus sequence construction from multiple sequence alignment
  I am writing a function which takes aligned sequences, and outputs a consensus sequence using IUP...
• Two Plink map/ped files refuse to merge.
  Two map/ped files refused to merge for some reason. I followed this method here (https://www.bio...