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• generate consensus sequence from unphased heterozygous calls
  I'd like to generate a single consensus by substituting a set of unphased snp and indel variant c...
• TRANSDECODER v5.0.2 - nucleotide sequences with ambiguity characters S,R,W,K, Y
  Hello, I download 30 coding sequences genomes of different species from Ensembl or NCBI. In or...
• Mapping To Genome With Ambiguous Reference Characters (R,Y,K,M,S,W Etc.)
  I am mapping illumina reads using bowtie/bwa to a reference genome with ambiguous reference chara...
• Remove ambiguous calls in the VCF file
  Hi everyone, I have a VCF file with multiple ambiguous ref/alt calls at some positions of the ge...
• Venndiagram Using R
  Could anyone would be able to guide me to draw a venn diagram with five entries with R library Ve...
• AA prediction from CDR3 DNA sequence
  Hi, I was trying to figure out how CDR3 DNA sequence in TCR sequencing is converted to the corres...
• Understanding a blast output
  `enter code here`I performed a genome blast and saved the results for each chromosome in a .xml f...
• Understanding a blast output
  I performed a genome blast and saved the results for each chromosome in a .xml file. For each gen...
• Calculation of heterozygosity at multi allelic region from 1000 Genomes data
  Hi all, I would like to ask how to calculate heterozygosity from 1000 genomes data. In the ENCO...
• Estimate the genome heterozygosity from a PacBio dataset
  Hi! I know that in the case of Illumina sequences it is possible to use jellyfish for the k-mers...
• betweenLaneNormalization and calcNormFactors in RUVs
  I'm analyzing the RNAseq data using the RUVs tutorial. In this tutorial they use two functions, ...
• improve my slow R function
  I am trying to calculate the percentage of heterozygous sites for each sample. I wrote a R script...
• Where does Kmergenie get it's y axis numbers from? Is it suppose to be the local maxima of each plot?
  This may sound rudimentary, but where is KmerGenie getting it's y-axis (number of genomic k-mers)...
• how to estimate heterozygosity by sample from a multi-sample vcf file
  Hi All, I want to estimate heterozygosity by samples from a multisample vcf file. I mapped whole-...
• What does '*' Amino Acid in BLOSUM Matrix of MATLAB mean?
  The BLOSUM(n) [e.g. BLOSUM(62)] returns a 24 by 24 matrix with the following amino acid sequence ...
• SNPEFF genome build with specific codon usage
  Failing to build my own Arabidopsis thaliana reference with Mt using 'codon.Mitochondrial' and Pt...
• Heterozygosity in k-mer histogram
  Hi! I ran GenomeScope to try to estimate the level of heterozygosity in my genome, however, the ...
• Calculation of P2 values for finding the mutational role in codon usage bias.
  I am working on finding codon usage bias and its determining factors in my species. Foe calculati...