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• Dataset format conversion from fastq to bam and vcf
  Hello, I am a begginer in the galaxy and I want to ask you how can I convert fastq files to bam ...
• galaxy full details
  describe about fastqc,fastq groomer, bwa ilumima, sam tools, mpileup, varscan, vcf filter, plz te...
• BAM to VCF format
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• VCF output from Mpileup tool
  Hi everyboy, I am trying to call SNP using the SAM Tools → mpileup in Galaxy. Since the input ...
• MAF to VCF showing Indels and snps
  Using Lastl I aligned a filtered fastq of mutant DNA to fasta of a reference chromosome. The alig...
• galaxy doesn't recognise dbSNP file I uploaded
  Hi I'm somewhat new to the game and struggling with the GATK unified genotyper. I found a dbsnp...
• Batch workflow with two different inputs each time?
  Dear Galaxy Community, I have actually installed Galaxy on our cluster, and I am now trying to d...
• GWAS: Fastq to BAM to VCF
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• BCFtools output tabular
  Hi, I'm sorry for my naive question (but this is my first analysis)... Analysis: 19 PCR targett...
• I cannot upload files from my pc in my new workflow
  I have just made a new workflow in Galaxy in order to convert a FASTQ file to VCF. In "Get Data" ...
• BWA for Illumina
  Hello, I'm starting to use Galaxy, and I'm trying to generate vcf and BAM files from my Fastq (pa...
• RNAseq data mapping to reference genome
  Hello, I have some RNAseq Illumina fastq data. I would like to align it to the referece genome o...
• pileup to vcf
  Is there a tool on public galaxy that will take pileup file or filter pileup output to VCF?
• Bcf To Vcf
  I wasw wondering if there is any option in Glaxy to convert bcf format to vcf format? Thanks Ka...
• VCF to Interval dataset
  Could anyone tell me how to convert a VCF dataset into Interval dataset on main galaxy? Thanks!!!
• VCF files not recognised by Gemini
  I uploaded few VCF files (VCF 4.1) generated by Illumina MiSeq to Galaxy. Although Galaxy recogni...
• tutorial to use VCF filters
  hi !!  are there videos, slides course material that talk about usage of VCF filter in galaxy
• MPileup calling every base as <X>
  Having a few teething problems on my first use of Galaxy (surprise!)   Workflow as follows; Up...
• 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...
• VCF file how to upload vcf file from Galaxy to my computer
  How to upload vcf single file from Galaxy to my computer?  Slavica Tankosic
• dna vcf file
  I was just wondering if anyone could help me with my vcf file. I would appreciate it. Thanks
• TAB to VCF
  Hi, I have a TAB delimited file. How can I convert it into a VCF format for downstream usage. T...