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• SNP calling in non-model organism
  hi I want to calling SNP in my RNAseq Data in my plant sample. my plant don't have reference geno...
• How To Call Snp And Indel Based On A Sanger Sequences Based Bac Contig Vs Reference?
  I have BAC contig, assembled from sanger sequences, that I want to use for quality control on my ...
• unigene assembly for snp calling
  I have a generic quetion regarding SNP calling for RNA seq data. Generally, the reference genome ...
• Contig/Scaffold Length- Variant Calling
  In our lab we have preliminary assembly on non-model genome organism. In the assembled genome, l...
• Making a custom reference genome
  Hi all,   For certain reasons, I need to make a custom reference genome to align my Illumina se...
• 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...
• Investigating a genome assembly
  Hello, I have to work with a genome assembly which consists of about 32000 scaffolds (obviously,...
• Should I retain ORFs predicted on minus strand of transcripts which assembled from strand-specific RNA-seq ?
  Hi,  I assembled a transcriptome using Trinity with  setting of --SS_lib_type R, then I continue...
• How To Call Snp From .Ab1 Files Of Sanger Sequencing?
  I've got a bunch of .ab1 files from sanger sequencing over an exon. Any free programs to quickly ...
• How to use samtools to assembly a gene?
  Hi,  I'm a new comer for samtools.  Here's the question: we got the raw data (reads) from sever...
• DiscoSNP++ results analysis
  Hi all, I have just started using the DiscoSNP++ tool. I have been facing some problems after i ...
• snp calling from faa file
  Hello there I am a noob to WGS. I am studying bacteria The bug I am studying is quite variable...
• Bacterial SNP calling pipeline with SNP and indels confirmation
  The outputs of my experiment would be getting SNPs and gaps for a set of 4 bacterial phenotypic v...
• SNPs detection in transcriptomics to define genetic variation between individuals
  Hi, I am new to the SNP calling analysis and my question regard "expectations". I am trying to c...
• Confusion with High Confidence SNP Calls (Overlap B/w RNA-seq & WGBS calls) and Genome Assemblies Used for Alignment and Annotation
  Hi! Here is what I have, I have SNP calls from RNA-Seq (paired end) and SNP calls from WGBS perf...
• Substituting Snps On Reference Genome Assemblies
  Hi again guys! So this time with a new question. I have a list of variant calls (basically, SNPs...
• A Question About Hybrid/Mix -Genome Assembly
  Hi There, Recently I have been trying to improve a genome assembly. It is a plant genome. It was...
• Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
  Does anyone here have experience using GATK for SNP and indel calling on an inbred species? Do y...
• Are there minimum requirements from a de novo genome assembly for it to be suitably used as a reference for SNP calling?
  To what extent does a de novo genome need to be assembled for it to be used as a reference? If I ...
• Masking phages, mobile elements, and transposons before calling SNP's
  I need to mask phages, mobile elements, and transposons before calling SNP's in my bacterial geno...