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• How to extract SNPs from galaxy workflow
  I exactly followed the below galaxy workflow that contain targetted re-sequencing data for a fath...
• Extract SNPs flanking sequence from organisme without reference genome
  Hi, I'm new in managing DNA sequences and I'm looking for help. I have fastq and vcf files from t...
• How To Extract Geneid From Pileup File?
  Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. ...
• How to separate SNPs from other variant types in Galaxy?
  I have a VCF file with all the called variants. I want to keep just the SNPs. This is achievable ...
• getting number of SNPs, insertion/deletion from VCF with VCFfilter
  Hello, I am trying to extract from a VCF file the number of SNPs: Single nucleotide variants , I...
• Regrading Snps
  I wish to compare SNPs in my mouse sample (SNP file generated from Partek Genomic suite) with SNP...
• Extracting reads from SNP list
  Hi Galaxy experts I am working on a non-model species and have created a denovo transcriptome as...
• SNPs genomic DNA
  Hi friends In my research project I am undertaking I have mined about 200,000 SNPs. I have extr...
• Extracting reads from SNP list
  Hi Galaxy experts I am working on a non-model species and have created a denovo transcriptome as...
• Snps And Conservation
  Hi, I'm trying to investigate conservation in SNPs using Galaxy, but running into a few "issues"...
• Filter Crash
  Hi! I use galaxy 2.2 I extract all snps from snp125 (whole genome, hg17, i use ucsc browser mai...
• Extract assembled transcripts from Cufflinks gtf without to use reference genome
  Hi all, I know there were similar questions, but unfortunately I couldn't find proper answer for...
• Need help with Circos plotting of snps on Galaxy
  Please help me to make a Circos plot of snps against the reference genome on Galaxy. I have a bed...
• SNP Genomic Interval Intersect Error
  Hi all, Please indulge a question from new user. I have a .bed of SNPs with annotations, and wan...
• How to extract information from a VCF file
  Hi everyone, I am currently taking an online tutorial on Galaxy and I have managed to complete s...
• Flanking regions from SNP list
  Hello  Using the RNA seq data and have performed de novo assembly with non-model species. I have...
• Ngs: Indel Analysis Tool Order
  Hello! I have a question about the NGS: Indel Analysis toolset in Galaxy. I hav...
• visualizing a VCF dataset
  Hiiii, i have made a vcf file and has filtered SNPs from there. Now, the problem is i am trying t...
• Get Flanks skipped invalid lines
  Hello Galaxy Experts I have a query regarding "Get flanks" tool under "Operate on genomic inter...
• Identifying relevant SNPs from a list
  I have a list of all SNPs in CDS of several thousand genes, and I'm looking for a convenient meth...
• SNPs associated with a gene
  Dear All, which tool is recommended to use for finding out which SNPs associated with which gene...
• Extracting files from .dat archives
  Hi, I downloaded a Galaxy history to my local disk and it saves as a .dat file. The history cont...
• Extract reads from BAM file
  Hi I have a BAM file with all the reads aligned to the reference sequence that I used to map them...
• extract fasta file from Galaxy
  I am trying to extract fasta file from galaxy after cuffcompare analysis which gave me combined t...