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• Whole Exome From Whole Genome
  Is there a way I can extract whole exome portions from the whole genome data using any standard t...
• Whole Exome Sequencing Depth
  Hi, I want to calculate Copy number variations(CNV) from Whole exome seq data. What is the corr...
• Derive Protein Domain Sequence From Personal Exome Data
  I am interested in a particular protein domain and I would like to extract all instance of this d...
• How to assess information content / mutual information between 2 sets of variables ?
  Am testing data from a clinical device; data was extracted using two complementary methods    ...
• eigengenes query on rationale
  I have been studying the package WGCNA in R. This package was developed with the idea that one co...
• Tools For De Novo Assembly For Exome Sequencing Data
  I'm using some tools such as Pindel to call structural variants from exome data. Since exome is s...
• What Genetic Marker To Use To Infer Pedigree From Sequencing Data?
  Here's a unusual tricky question. Now I've got whole-exome sequencing data for 5 individuals fro...
• Biological variation within replicate groups, not much DE
  Dear all, I recently conducted an experiment and there seems to be quite some variation within r...
• Genotype Data And Exome Sequencing Data Sensitivity
  I genotyped a sample by Illumina SNP array and I sequenced its exome sequencing data. What is the...
• Copy number variation detection tools within exome sequencing
  Hi. I would like to search copy number variation using exome sequence data. I have been using V...
• Does whole exome bam files in TCGA have unpaired reads?
  I am trying to slice some whole exome bam files from TCGA and for my pipeline I need to extract ...
• sea corrected expression matrix
  I'm using sva to remove batch effects on microarray data. I don't want to do differential gene ex...
• How to phase a WGS dataset preserving the indels within it?
  Hi all, I have a WGS dataset in which indels were also called. Now I am looking towards creating...
• How to extract reads that map within a defined interval from each other
  I have paired end sequence data which I have mapped to a reference. I need to extract reads from ...
• Exome and UTRs
  Hi,  I wonder, can we use Exome sequencing data to capture UTR polymorphisms?  I am interested ...
• Mouse exome sequencing: download fastq?
  Hi, I would like to study fastq sequences from mouse exome sequencing. Do you know where I can d...
• A method for extracting two variable regions from a FASTA file containing long reads (see image)
  Hi all, I'm looking for help or suggestions regarding a technique for extracting the variable r...
• Where can I get exome vcf file from the 1000 genome project?
  Hi, I'm trying to use 1000 genome data as control data for my analysis. I am interested in exome ...
• Identifying contaminants (cow, pig) in oral rinse exome sequencing data
  I have exome sequencing data for oral rinse samples tested for hereditary cancers. I am looking f...
• Extract SNPs within 5 bps distance apart
  Hi, I am wondering is there a way to extract / print those variants from a vcf file whose distan...
• calculate mutation burden per gene
  Dear all, I have a list of genes for which I want to calculate the mutations per MB. How do I d...
• Pathway Annotation for variants Exome Data
  Hello, I have exome results and I would have liked to detect the pathway with the most mutations...